Bio.Blast.Applications module

Definitions for interacting with BLAST related applications (OBSOLETE).

Wrappers for the new NCBI BLAST+ tools (written in C++):

• NcbiblastpCommandline - Protein-Protein BLAST

• NcbiblastnCommandline - Nucleotide-Nucleotide BLAST

• NcbiblastxCommandline - Translated Query-Protein Subject BLAST

• NcbitblastnCommandline - Protein Query-Translated Subject BLAST

• NcbitblastxCommandline - Translated Query-Protein Subject BLAST

• NcbipsiblastCommandline - Position-Specific Initiated BLAST

• NcbirpsblastCommandline - Reverse Position Specific BLAST

• NcbirpstblastnCommandline - Translated Reverse Position Specific BLAST

• NcbideltablastCommandline - Protein-Protein domain enhanced lookup time accelerated blast

• NcbiblastformatterCommandline - Convert ASN.1 to other BLAST output formats

• NcbimakeblastdbCommandline - Application to create BLAST databases

For further details, see:

Camacho et al. BLAST+: architecture and applications BMC Bioinformatics 2009, 10:421 https://doi.org/10.1186/1471-2105-10-421

We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.

class Bio.Blast.Applications.NcbiblastpCommandline(cmd='blastp', **kwargs)

Bases: _NcbiblastMain2SeqCommandline

Create a commandline for the NCBI BLAST+ program blastp (for proteins).

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastp.

>>> from Bio.Blast.Applications import NcbiblastpCommandline
>>> cline = NcbiblastpCommandline(query="rosemary.pro", db="nr",
...                               evalue=0.001, remote=True, ungapped=True)
>>> cline
NcbiblastpCommandline(cmd='blastp', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True)
>>> print(cline)
blastp -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='blastp', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics (string, default 2, i.e. True).

0, F or f: no composition-based statistics

2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties

Note that tblastn also supports values of 1 and 3.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property db_hard_mask

Filtering algorithm for hard masking (integer).

Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc

This controls the addition of the -db_hard_mask parameter and its associated value. Set this property to the argument value required.

property db_soft_mask

Filtering algorithm for soft masking (integer).

Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_loc

This controls the addition of the -db_soft_mask parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property task

Task to execute (string, blastp (default), blastp-fast or blastp-short).

This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property ungapped

Perform ungapped alignment only?

This property controls the addition of the -ungapped switch, treat this property as a boolean.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbiblastnCommandline(cmd='blastn', **kwargs)

Bases: _NcbiblastMain2SeqCommandline

Wrapper for the NCBI BLAST+ program blastn (for nucleotides).

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastn.

For example, to run a search against the “nt” nucleotide database using the FASTA nucleotide file “m_code.fasta” as the query, with an expectation value cut off of 0.001, saving the output to a file in XML format:

>>> from Bio.Blast.Applications import NcbiblastnCommandline
>>> cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus",
...                               evalue=0.001, out="m_cold.xml", outfmt=5)
>>> cline
NcbiblastnCommandline(cmd='blastn', out='m_cold.xml', outfmt=5, query='m_cold.fasta', db='nt', evalue=0.001, strand='plus')
>>> print(cline)
blastn -out m_cold.xml -outfmt 5 -query m_cold.fasta -db nt -evalue 0.001 -strand plus

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='blastn', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property db_hard_mask

Filtering algorithm for hard masking (integer).

Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc

This controls the addition of the -db_hard_mask parameter and its associated value. Set this property to the argument value required.

property db_soft_mask

Filtering algorithm for soft masking (integer).

Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_loc

This controls the addition of the -db_soft_mask parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property dust

Filter query sequence with DUST (string).

Format: ‘yes’, ‘level window linker’, or ‘no’ to disable.

Default = ‘20 64 1’.

This controls the addition of the -dust parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property filtering_db

BLAST database containing filtering elements (i.e. repeats).

This controls the addition of the -filtering_db parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property index_name

MegaBLAST database index name.

This controls the addition of the -index_name parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property min_raw_gapped_score

Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages (integer).

This controls the addition of the -min_raw_gapped_score parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property no_greedy

Use non-greedy dynamic programming extension

This property controls the addition of the -no_greedy switch, treat this property as a boolean.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property off_diagonal_range

Number of off-diagonals to search for the 2nd hit (integer).

Expects a positive integer, or 0 (default) to turn off.Added in BLAST 2.2.23+

This controls the addition of the -off_diagonal_range parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property penalty

Penalty for a nucleotide mismatch (integer, at most zero).

This controls the addition of the -penalty parameter and its associated value. Set this property to the argument value required.

property perc_identity

Percent identity (real, 0 to 100 inclusive).

This controls the addition of the -perc_identity parameter and its associated value. Set this property to the argument value required.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property reward

Reward for a nucleotide match (integer, at least zero).

This controls the addition of the -reward parameter and its associated value. Set this property to the argument value required.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property strand

Query strand(s) to search against database/subject.

Values allowed are “both” (default), “minus”, “plus”.

This controls the addition of the -strand parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property task

Task to execute (string, default ‘megablast’)

Allowed values ‘blastn’, ‘blastn-short’, ‘dc-megablast’, ‘megablast’ (the default), or ‘vecscreen’.

This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

property template_length

Discontiguous MegaBLAST template length (integer).

Allowed values: 16, 18, 21.

Requires: template_type.

This controls the addition of the -template_length parameter and its associated value. Set this property to the argument value required.

property template_type

Discontiguous MegaBLAST template type (string).

Allowed values: ‘coding’, ‘coding_and_optimal’ or ‘optimal’. Requires: template_length.

This controls the addition of the -template_type parameter and its associated value. Set this property to the argument value required.

property ungapped

Perform ungapped alignment only?

This property controls the addition of the -ungapped switch, treat this property as a boolean.

property use_index

Use MegaBLAST database index (Boolean, Default = False)

This controls the addition of the -use_index parameter and its associated value. Set this property to the argument value required.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_masker_db

Enable WindowMasker filtering using this repeats database (string).

This controls the addition of the -window_masker_db parameter and its associated value. Set this property to the argument value required.

property window_masker_taxid

Enable WindowMasker filtering using a Taxonomic ID (integer).

This controls the addition of the -window_masker_taxid parameter and its associated value. Set this property to the argument value required.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbiblastxCommandline(cmd='blastx', **kwargs)

Bases: _NcbiblastMain2SeqCommandline

Wrapper for the NCBI BLAST+ program blastx (nucleotide query, protein database).

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p blastx.

>>> from Bio.Blast.Applications import NcbiblastxCommandline
>>> cline = NcbiblastxCommandline(query="m_cold.fasta", db="nr", evalue=0.001)
>>> cline
NcbiblastxCommandline(cmd='blastx', query='m_cold.fasta', db='nr', evalue=0.001)
>>> print(cline)
blastx -query m_cold.fasta -db nr -evalue 0.001

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='blastx', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics for blastp, blastx, or tblastn.

D or d: default (equivalent to 2 )

0 or F or f: no composition-based statistics

1: Composition-based statistics as in NAR 29:2994-3005, 2001

2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties

3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.

For programs other than tblastn, must either be absent or be D, F or 0

Default = 2.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property db_hard_mask

Filtering algorithm for hard masking (integer).

Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc

This controls the addition of the -db_hard_mask parameter and its associated value. Set this property to the argument value required.

property db_soft_mask

Filtering algorithm for soft masking (integer).

Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_loc

This controls the addition of the -db_soft_mask parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property frame_shift_penalty

Frame shift penalty (integer, at least 1, default ignored) (OBSOLETE).

This was removed in BLAST 2.2.27+

This controls the addition of the -frame_shift_penalty parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_intron_length

Maximum intron length (integer).

Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking). Default zero.

This controls the addition of the -max_intron_length parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_gencode

Genetic code to use to translate query (integer, default 1).

This controls the addition of the -query_gencode parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable.Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property strand

Query strand(s) to search against database/subject.

Values allowed are “both” (default), “minus”, “plus”.

This controls the addition of the -strand parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property task

Task to execute (string, blastx (default) or blastx-fast).

This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property ungapped

Perform ungapped alignment only?

This property controls the addition of the -ungapped switch, treat this property as a boolean.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbitblastnCommandline(cmd='tblastn', **kwargs)

Bases: _NcbiblastMain2SeqCommandline

Wrapper for the NCBI BLAST+ program tblastn.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p tblastn.

>>> from Bio.Blast.Applications import NcbitblastnCommandline
>>> cline = NcbitblastnCommandline(help=True)
>>> cline
NcbitblastnCommandline(cmd='tblastn', help=True)
>>> print(cline)
tblastn -help

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='tblastn', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics (string, default 2, i.e. True).

0, F or f: no composition-based statistics

1: Composition-based statistics as in NAR 29:2994-3005, 2001

2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties

3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally

Note that only tblastn supports values of 1 and 3.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property db_gencode

Genetic code to use to translate query (integer, default 1).

This controls the addition of the -db_gencode parameter and its associated value. Set this property to the argument value required.

property db_hard_mask

Filtering algorithm for hard masking (integer).

Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc

This controls the addition of the -db_hard_mask parameter and its associated value. Set this property to the argument value required.

property db_soft_mask

Filtering algorithm for soft masking (integer).

Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_loc

This controls the addition of the -db_soft_mask parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property frame_shift_penalty

Frame shift penalty (integer, at least 1, default ignored) (OBSOLETE).

This was removed in BLAST 2.2.27+

This controls the addition of the -frame_shift_penalty parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property in_pssm

PSI-BLAST checkpoint file.

Incompatible with: remote, query

This controls the addition of the -in_pssm parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_intron_length

Maximum intron length (integer).

Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking). Default zero.

This controls the addition of the -max_intron_length parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable.

Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property task

Task to execute (string, tblastn (default) or tblastn-fast).

This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property ungapped

Perform ungapped alignment only?

This property controls the addition of the -ungapped switch, treat this property as a boolean.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbitblastxCommandline(cmd='tblastx', **kwargs)

Bases: _NcbiblastMain2SeqCommandline

Wrapper for the NCBI BLAST+ program tblastx.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastall tool with separate tools for each of the searches. This wrapper therefore replaces BlastallCommandline with option -p tblastx.

>>> from Bio.Blast.Applications import NcbitblastxCommandline
>>> cline = NcbitblastxCommandline(help=True)
>>> cline
NcbitblastxCommandline(cmd='tblastx', help=True)
>>> print(cline)
tblastx -help

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='tblastx', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property db_gencode

Genetic code to use to translate query (integer, default 1).

This controls the addition of the -db_gencode parameter and its associated value. Set this property to the argument value required.

property db_hard_mask

Filtering algorithm for hard masking (integer).

Filtering algorithm ID to apply to BLAST database as hard masking. Incompatible with: db_soft_mask, subject, subject_loc

This controls the addition of the -db_hard_mask parameter and its associated value. Set this property to the argument value required.

property db_soft_mask

Filtering algorithm for soft masking (integer).

Filtering algorithm ID to apply to BLAST database as soft masking. Incompatible with: db_hard_mask, subject, subject_loc

This controls the addition of the -db_soft_mask parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_intron_length

Maximum intron length (integer).

Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking). Default zero.

This controls the addition of the -max_intron_length parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_gencode

Genetic code to use to translate query (integer, default 1).

This controls the addition of the -query_gencode parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable.

Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property strand

Query strand(s) to search against database/subject.

Values allowed are “both” (default), “minus”, “plus”.

This controls the addition of the -strand parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbipsiblastCommandline(cmd='psiblast', **kwargs)

Bases: _Ncbiblast2SeqCommandline

Wrapper for the NCBI BLAST+ program psiblast.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old blastpgp tool with a similar tool psiblast. This wrapper therefore replaces BlastpgpCommandline, the wrapper for blastpgp.

>>> from Bio.Blast.Applications import NcbipsiblastCommandline
>>> cline = NcbipsiblastCommandline(help=True)
>>> cline
NcbipsiblastCommandline(cmd='psiblast', help=True)
>>> print(cline)
psiblast -help

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='psiblast', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics (string, default 2, i.e. True).

0, F or f: no composition-based statistics

2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties

Note that tblastn also supports values of 1 and 3.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gap_trigger

Number of bits to trigger gapping (float, default 22).

This controls the addition of the -gap_trigger parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property ignore_msa_master

Ignore the master sequence when creating PSSM.

Requires: in_msa Incompatible with: msa_master_idx, in_pssm, query, query_loc, phi_pattern

This property controls the addition of the -ignore_msa_master switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property in_msa

File name of multiple sequence alignment to restart PSI-BLAST.

Incompatible with: in_pssm, query

This controls the addition of the -in_msa parameter and its associated value. Set this property to the argument value required.

property in_pssm

PSI-BLAST checkpoint file.

Incompatible with: in_msa, query, phi_pattern

This controls the addition of the -in_pssm parameter and its associated value. Set this property to the argument value required.

property inclusion_ethresh

E-value inclusion threshold for pairwise alignments (float, default 0.002).

This controls the addition of the -inclusion_ethresh parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property msa_master_idx

Index of sequence to use as master in MSA.

Index (1-based) of sequence to use as the master in the multiple sequence alignment. If not specified, the first sequence is used.

This controls the addition of the -msa_master_idx parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_iterations

Number of iterations to perform (integer, at least one).

Default is one. Incompatible with: remote

This controls the addition of the -num_iterations parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property out_ascii_pssm

File name to store ASCII version of PSSM.

This controls the addition of the -out_ascii_pssm parameter and its associated value. Set this property to the argument value required.

property out_pssm

File name to store checkpoint file.

This controls the addition of the -out_pssm parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property phi_pattern

File name containing pattern to search.

Incompatible with: in_pssm

This controls the addition of the -phi_pattern parameter and its associated value. Set this property to the argument value required.

property pseudocount

Pseudo-count value used when constructing PSSM.

Integer. Default is zero.

This controls the addition of the -pseudocount parameter and its associated value. Set this property to the argument value required.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property save_each_pssm

Save PSSM after each iteration

File name is given in -save_pssm or -save_ascii_pssm options.

This property controls the addition of the -save_each_pssm switch, treat this property as a boolean.

property save_pssm_after_last_round

Save PSSM after the last database search.

This property controls the addition of the -save_pssm_after_last_round switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable. Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbirpsblastCommandline(cmd='rpsblast', **kwargs)

Bases: _NcbiblastCommandline

Wrapper for the NCBI BLAST+ program rpsblast.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old rpsblast tool with a similar tool of the same name. This wrapper replaces RpsBlastCommandline, the wrapper for the old rpsblast.

>>> from Bio.Blast.Applications import NcbirpsblastCommandline
>>> cline = NcbirpsblastCommandline(help=True)
>>> cline
NcbirpsblastCommandline(cmd='rpsblast', help=True)
>>> print(cline)
rpsblast -help

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='rpsblast', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (recommended value: 0.1).

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (recommended value: 0.1).

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics.

D or d: default (equivalent to 0)

0 or F or f: Simplified Composition-based statistics as in Bioinformatics 15:1000-1011, 1999

1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001

Default = 0.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable.Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbirpstblastnCommandline(cmd='rpstblastn', **kwargs)

Bases: _NcbiblastCommandline

Wrapper for the NCBI BLAST+ program rpstblastn.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI replaced the old rpsblast tool with a similar tool of the same name, and a separate tool rpstblastn for Translated Reverse Position Specific BLAST.

>>> from Bio.Blast.Applications import NcbirpstblastnCommandline
>>> cline = NcbirpstblastnCommandline(help=True)
>>> cline
NcbirpstblastnCommandline(cmd='rpstblastn', help=True)
>>> print(cline)
rpstblastn -help

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='rpstblastn', **kwargs)

Initialize the class.

property comp_based_stats

Use composition-based statistics.

D or d: default (equivalent to 0)

0 or F or f: Simplified Composition-based statistics as in Bioinformatics 15:1000-1011, 1999

1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001

Default = 0.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_gencode

Genetic code to use to translate query (integer, default 1).

This controls the addition of the -query_gencode parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable. Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property strand

Query strand(s) to search against database/subject.

Values allowed are “both” (default), “minus”, “plus”.

This controls the addition of the -strand parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property ungapped

Perform ungapped alignment only?

This property controls the addition of the -ungapped switch, treat this property as a boolean.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbiblastformatterCommandline(cmd='blast_formatter', **kwargs)

Bases: _NcbibaseblastCommandline

Wrapper for the NCBI BLAST+ program blast_formatter.

With the release of BLAST 2.2.24+ (i.e. the BLAST suite rewritten in C++ instead of C), the NCBI added the ASN.1 output format option to all the search tools, and extended the blast_formatter to support this as input.

The blast_formatter command allows you to convert the ASN.1 output into the other output formats (XML, tabular, plain text, HTML).

>>> from Bio.Blast.Applications import NcbiblastformatterCommandline
>>> cline = NcbiblastformatterCommandline(archive="example.asn", outfmt=5, out="example.xml")
>>> cline
NcbiblastformatterCommandline(cmd='blast_formatter', out='example.xml', outfmt=5, archive='example.asn')
>>> print(cline)
blast_formatter -out example.xml -outfmt 5 -archive example.asn

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

Note that this wrapper is for the version of blast_formatter from BLAST 2.2.24+ (or later) which is when the NCBI first announced the inclusion this tool. There was actually an early version in BLAST 2.2.23+ (and possibly in older releases) but this did not have the -archive option (instead -rid is a mandatory argument), and is not supported by this wrapper.

__init__(cmd='blast_formatter', **kwargs)

Initialize the class.

property archive

Archive file of results, not compatible with rid arg.

This controls the addition of the -archive parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep.

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property rid

BLAST Request ID (RID), not compatible with archive arg.

This controls the addition of the -rid parameter and its associated value. Set this property to the argument value required.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

class Bio.Blast.Applications.NcbideltablastCommandline(cmd='deltablast', **kwargs)

Bases: _Ncbiblast2SeqCommandline

Create a commandline for the NCBI BLAST+ program deltablast (for proteins).

This is a wrapper for the deltablast command line command included in the NCBI BLAST+ software (not present in the original BLAST).

>>> from Bio.Blast.Applications import NcbideltablastCommandline
>>> cline = NcbideltablastCommandline(query="rosemary.pro", db="nr",
...                               evalue=0.001, remote=True)
>>> cline
NcbideltablastCommandline(cmd='deltablast', query='rosemary.pro', db='nr', evalue=0.001, remote=True)
>>> print(cline)
deltablast -query rosemary.pro -db nr -evalue 0.001 -remote

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='deltablast', **kwargs)

Initialize the class.

property best_hit_overhang

Best Hit algorithm overhang value (float, recommended value: 0.1)

Float between 0.0 and 0.5 inclusive. Incompatible with: culling_limit.

This controls the addition of the -best_hit_overhang parameter and its associated value. Set this property to the argument value required.

property best_hit_score_edge

Best Hit algorithm score edge value (float).

Float between 0.0 and 0.5 inclusive. Recommended value: 0.1

Incompatible with: culling_limit.

This controls the addition of the -best_hit_score_edge parameter and its associated value. Set this property to the argument value required.

property comp_based_stats

Use composition-based statistics (string, default 2, i.e. True).

0, F or f: no composition-based statistics.

2, T or t, D or d : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties

Note that tblastn also supports values of 1 and 3.

This controls the addition of the -comp_based_stats parameter and its associated value. Set this property to the argument value required.

property culling_limit

Hit culling limit (integer).

If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.

Incompatible with: best_hit_overhang, best_hit_score_edge.

This controls the addition of the -culling_limit parameter and its associated value. Set this property to the argument value required.

property db

The database to BLAST against.

This controls the addition of the -db parameter and its associated value. Set this property to the argument value required.

property dbsize

Effective length of the database (integer).

This controls the addition of the -dbsize parameter and its associated value. Set this property to the argument value required.

property domain_inclusion_ethresh

E-value inclusion threshold for alignments with conserved domains.

(float, Default is 0.05)

This controls the addition of the -domain_inclusion_ethresh parameter and its associated value. Set this property to the argument value required.

property entrez_query

Restrict search with the given Entrez query (requires remote).

This controls the addition of the -entrez_query parameter and its associated value. Set this property to the argument value required.

property evalue

Expectation value cutoff.

This controls the addition of the -evalue parameter and its associated value. Set this property to the argument value required.

property export_search_strategy

File name to record the search strategy used.

Incompatible with: import_search_strategy

This controls the addition of the -export_search_strategy parameter and its associated value. Set this property to the argument value required.

property gap_trigger

Number of bits to trigger gapping. Default = 22.

This controls the addition of the -gap_trigger parameter and its associated value. Set this property to the argument value required.

property gapextend

Cost to extend a gap (integer).

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Cost to open a gap (integer).

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property gilist

Restrict search of database to list of GI’s.

Incompatible with: negative_gilist, seqidlist, negative_seqidlist, remote, subject, subject_loc

This controls the addition of the -gilist parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property html

Produce HTML output? See also the outfmt option.

This property controls the addition of the -html switch, treat this property as a boolean.

property import_search_strategy

Search strategy to use.

Incompatible with: export_search_strategy

This controls the addition of the -import_search_strategy parameter and its associated value. Set this property to the argument value required.

property inclusion_ethresh

Pairwise alignment e-value inclusion threshold (float, default 0.002).

This controls the addition of the -inclusion_ethresh parameter and its associated value. Set this property to the argument value required.

property lcase_masking

Use lower case filtering in query and subject sequence(s)?

This property controls the addition of the -lcase_masking switch, treat this property as a boolean.

property line_length

Line length for formatting alignments (integer, at least 1, default 60).

Not applicable for outfmt > 4. Added in BLAST+ 2.2.30.

This controls the addition of the -line_length parameter and its associated value. Set this property to the argument value required.

property matrix

Scoring matrix name (default BLOSUM62).

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property max_hsps

Set max number of HSPs saved per subject sequence

Ddefault 0 means no limit.

This controls the addition of the -max_hsps parameter and its associated value. Set this property to the argument value required.

property max_hsps_per_subject

Override max number of HSPs per subject saved for ungapped searches (integer).

This controls the addition of the -max_hsps_per_subject parameter and its associated value. Set this property to the argument value required.

property max_target_seqs

Maximum number of aligned sequences to keep (integer, at least one).

This controls the addition of the -max_target_seqs parameter and its associated value. Set this property to the argument value required.

property negative_gilist

Restrict search of database to everything except the listed GIs.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_gilist parameter and its associated value. Set this property to the argument value required.

property negative_seqidlist

Restrict search of database to everything except listed SeqID’s.

Incompatible with: gilist, seqidlist, remote, subject, subject_loc

This controls the addition of the -negative_seqidlist parameter and its associated value. Set this property to the argument value required.

property num_alignments

Number of database sequences to show num_alignments for.

Integer argument (at least zero). Default is 200. See also num_alignments.

This controls the addition of the -num_alignments parameter and its associated value. Set this property to the argument value required.

property num_descriptions

Number of database sequences to show one-line descriptions for.

Integer argument (at least zero). Default is 500. See also num_alignments.

This controls the addition of the -num_descriptions parameter and its associated value. Set this property to the argument value required.

property num_iterations

Number of iterations to perform. (integer >=1, Default is 1).

Incompatible with: remote

This controls the addition of the -num_iterations parameter and its associated value. Set this property to the argument value required.

property num_threads

Number of threads to use in the BLAST search.

Integer, at least one. Default is one. Incompatible with: remote

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property out_ascii_pssm

File name to store ASCII version of PSSM.

This controls the addition of the -out_ascii_pssm parameter and its associated value. Set this property to the argument value required.

property out_pssm

File name to store checkpoint file.

This controls the addition of the -out_pssm parameter and its associated value. Set this property to the argument value required.

property outfmt

Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML).

This controls the addition of the -outfmt parameter and its associated value. Set this property to the argument value required.

property parse_deflines

Should the query and subject defline(s) be parsed?

This property controls the addition of the -parse_deflines switch, treat this property as a boolean.

property pseudocount

Pseudo-count value used when constructing PSSM (integer, default 0).

This controls the addition of the -pseudocount parameter and its associated value. Set this property to the argument value required.

property qcov_hsp_perc

Percent query coverage per hsp (float, 0 to 100).

Added in BLAST+ 2.2.30.

This controls the addition of the -qcov_hsp_perc parameter and its associated value. Set this property to the argument value required.

property query

The sequence to search with.

This controls the addition of the -query parameter and its associated value. Set this property to the argument value required.

property query_loc

Location on the query sequence (Format: start-stop).

This controls the addition of the -query_loc parameter and its associated value. Set this property to the argument value required.

property remote

Execute search remotely?

Incompatible with: gilist, negative_gilist, subject_loc, num_threads, …

This property controls the addition of the -remote switch, treat this property as a boolean.

property rpsdb

BLAST domain database name (dtring, Default = ‘cdd_delta’).

This controls the addition of the -rpsdb parameter and its associated value. Set this property to the argument value required.

property save_each_pssm

Save PSSM after each iteration.

File name is given in -save_pssm or -save_ascii_pssm options.

This property controls the addition of the -save_each_pssm switch, treat this property as a boolean.

property save_pssm_after_last_round

Save PSSM after the last database search.

This property controls the addition of the -save_pssm_after_last_round switch, treat this property as a boolean.

property searchsp

Effective length of the search space (integer).

This controls the addition of the -searchsp parameter and its associated value. Set this property to the argument value required.

property seg

Filter query sequence with SEG (string).

Format: “yes”, “window locut hicut”, or “no” to disable. Default is “12 2.2 2.5”

This controls the addition of the -seg parameter and its associated value. Set this property to the argument value required.

property seqidlist

Restrict search of database to list of SeqID’s.

Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

This controls the addition of the -seqidlist parameter and its associated value. Set this property to the argument value required.

property show_domain_hits

Show domain hits?

Incompatible with: remote, subject

This property controls the addition of the -show_domain_hits switch, treat this property as a boolean.

property show_gis

Show NCBI GIs in deflines?

This property controls the addition of the -show_gis switch, treat this property as a boolean.

property soft_masking

Apply filtering locations as soft masks (Boolean, Default = true).

This controls the addition of the -soft_masking parameter and its associated value. Set this property to the argument value required.

property subject

Subject sequence(s) to search.

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask

See also subject_loc.

This controls the addition of the -subject parameter and its associated value. Set this property to the argument value required.

property subject_loc

Location on the subject sequence (Format: start-stop).

Incompatible with: db, gilist, seqidlist, negative_gilist, negative_seqidlist, db_soft_mask, db_hard_mask, remote.

See also subject.

This controls the addition of the -subject_loc parameter and its associated value. Set this property to the argument value required.

property sum_statistics

Use sum statistics.

This property controls the addition of the -sum_statistics switch, treat this property as a boolean.

property sum_stats

Use sum statistics (boolean).

Added in BLAST+ 2.2.30.

This controls the addition of the -sum_stats parameter and its associated value. Set this property to the argument value required.

property threshold

Minimum score for words to be added to the BLAST lookup table (float).

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property use_sw_tback

Compute locally optimal Smith-Waterman alignments?

This property controls the addition of the -use_sw_tback switch, treat this property as a boolean.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.

property window_size

Multiple hits window size, use 0 to specify 1-hit algorithm (integer).

This controls the addition of the -window_size parameter and its associated value. Set this property to the argument value required.

property word_size

Word size for wordfinder algorithm.

Integer. Minimum 2.

This controls the addition of the -word_size parameter and its associated value. Set this property to the argument value required.

property xdrop_gap

X-dropoff value (in bits) for preliminary gapped extensions (float).

This controls the addition of the -xdrop_gap parameter and its associated value. Set this property to the argument value required.

property xdrop_gap_final

X-dropoff value (in bits) for final gapped alignment (float).

This controls the addition of the -xdrop_gap_final parameter and its associated value. Set this property to the argument value required.

property xdrop_ungap

X-dropoff value (in bits) for ungapped extensions (float).

This controls the addition of the -xdrop_ungap parameter and its associated value. Set this property to the argument value required.

class Bio.Blast.Applications.NcbimakeblastdbCommandline(cmd='makeblastdb', **kwargs)

Bases: AbstractCommandline

Wrapper for the NCBI BLAST+ program makeblastdb.

This is a wrapper for the NCBI BLAST+ makeblastdb application to create BLAST databases. By default, this creates a blast database with the same name as the input file. The default output location is the same directory as the input.

>>> from Bio.Blast.Applications import NcbimakeblastdbCommandline
>>> cline = NcbimakeblastdbCommandline(dbtype="prot",
...                                    input_file="NC_005816.faa")
>>> cline
NcbimakeblastdbCommandline(cmd='makeblastdb', dbtype='prot', input_file='NC_005816.faa')
>>> print(cline)
makeblastdb -dbtype prot -in NC_005816.faa

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='makeblastdb', **kwargs)

Initialize the class.

property blastdb_version

Version of BLAST database to be created. Tip: use BLAST database version 4 on 32 bit CPU. Default = 5

This controls the addition of the -blastdb_version parameter and its associated value. Set this property to the argument value required.

property dbtype

Molecule type of target db (‘nucl’ or ‘prot’).

This controls the addition of the -dbtype parameter and its associated value. Set this property to the argument value required.

property gi_mask

Create GI indexed masking data.

This property controls the addition of the -gi_mask switch, treat this property as a boolean.

property gi_mask_name

Comma-separated list of masking data output files.

This controls the addition of the -gi_mask_name parameter and its associated value. Set this property to the argument value required.

property h

Print USAGE and DESCRIPTION; ignore other arguments.

This property controls the addition of the -h switch, treat this property as a boolean.

property hash_index

Create index of sequence hash values.

This property controls the addition of the -hash_index switch, treat this property as a boolean.

property help

Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.

This property controls the addition of the -help switch, treat this property as a boolean.

property input_file

Input file/database name.

This controls the addition of the -in parameter and its associated value. Set this property to the argument value required.

property input_type

Type of the data specified in input_file.

Default = ‘fasta’. Added in BLAST 2.2.26.

This controls the addition of the -input_type parameter and its associated value. Set this property to the argument value required.

property logfile

File to which the program log should be redirected.

This controls the addition of the -logfile parameter and its associated value. Set this property to the argument value required.

property mask_data

Comma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker).

This controls the addition of the -mask_data parameter and its associated value. Set this property to the argument value required.

property mask_desc

Comma-separated list of free form strings to describe the masking algorithm details.

This controls the addition of the -mask_desc parameter and its associated value. Set this property to the argument value required.

property mask_id

Comma-separated list of strings to uniquely identify the masking algorithm.

This controls the addition of the -mask_id parameter and its associated value. Set this property to the argument value required.

property max_file_sz

Maximum file size for BLAST database files. Default = ‘1GB’.

This controls the addition of the -max_file_sz parameter and its associated value. Set this property to the argument value required.

property out

Output file for alignment.

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property parse_seqids

Option to parse seqid for FASTA input if set.

For all other input types, seqids are parsed automatically

This property controls the addition of the -parse_seqids switch, treat this property as a boolean.

property taxid

Taxonomy ID to assign to all sequences.

This controls the addition of the -taxid parameter and its associated value. Set this property to the argument value required.

property taxid_map

Text file mapping sequence IDs to taxonomy IDs.

Format:<SequenceId> <TaxonomyId><newline>

This controls the addition of the -taxid_map parameter and its associated value. Set this property to the argument value required.

property title

Title for BLAST database.

This controls the addition of the -title parameter and its associated value. Set this property to the argument value required.

property version

Print version number; ignore other arguments.

This property controls the addition of the -version switch, treat this property as a boolean.