Bio.SearchIO.BlastIO package

Submodules

Module contents

Bio.SearchIO support for BLAST+ output formats.

This module adds support for parsing BLAST+ outputs. BLAST+ is a rewrite of NCBI’s legacy BLAST (Basic Local Alignment Search Tool), based on the NCBI C++ toolkit. The BLAST+ suite is available as command line programs or on NCBI’s web page.

Bio.SearchIO.BlastIO was tested on the following BLAST+ flavors and versions:

  • flavors: blastn, blastp, blastx, tblastn, tblastx

  • versions: 2.2.22+, 2.2.26+

You should also be able to parse outputs from a local BLAST+ search or from NCBI’s web interface. Although the module was not tested against all BLAST+, it should still be able to parse these other versions’ outputs. Please submit a bug report if you stumble upon an unparsable file.

Some output formats from the BLAST legacy suite (BLAST+’s predecessor) may still be parsed by this module. However, results are not guaranteed. You may try to use the Bio.Blast module to parse them instead.

More information about BLAST are available through these links:

Supported Formats

Bio.SearchIO.BlastIO supports the following BLAST+ output formats:

  • XML - ‘blast-xml’ - parsing, indexing, writing

  • Tabular - ‘blast-tab’ - parsing, indexing, writing

blast-xml

The blast-xml parser follows the BLAST XML DTD written here: http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd

It provides the following attributes for each SearchIO object:

Object

Attribute

XML Element

QueryResult

target

BlastOutput_db

program

BlastOutput_program

reference

BlastOutput_reference

version

BlastOutput_version [1]

description

Iteration_query-def

id

Iteration_query-ID

seq_len

Iteration_query-len

param_evalue_threshold

Parameters_expect

param_entrez_query

Parameters_entrez-query

param_filter

Parameters_filter

param_gap_extend

Parameters_gap-extend

param_gap_open

Parameters_gap-open

param_include

Parameters_include

param_matrix

Parameters_matrix

param_pattern

Parameters_pattern

param_score_match

Parameters_sc-match

param_score_mismatch

Parameters_sc-mismatch

stat_db_num

Statistics_db-num

stat_db_len

Statistics_db-len

stat_eff_space

Statistics_eff-space

stat_entropy

Statistics_entropy

stat_hsp_len

Statistics_hsp-len

stat_kappa

Statistics_kappa

stat_lambda

Statistics_lambda

Hit

accession

Hit_accession

description

Hit_def

id

Hit_id

seq_len

Hit_len

HSP

bitscore

Hsp_bit-score

density

Hsp_density

evalue

Hsp_evalue

gap_num

Hsp_gaps

ident_num

Hsp_identity

pos_num

Hsp_positive

bitscore_raw

Hsp_score

HSPFragment (also via HSP)

aln_span

Hsp_align-len

hit_frame

Hsp_hit-frame

hit_start

Hsp_hit-from

hit_end

Hsp_hit-to

hit

Hsp_hseq

aln_annotation

Hsp_midline

pattern_start

Hsp_pattern-from

pattern_end

Hsp_pattern-to

query_frame

Hsp_query-frame

query_start

Hsp_query-from

query_end

Hsp_query-to

query

Hsp_qseq

You may notice that in BLAST XML files, sometimes BLAST replaces your true sequence ID with its own generated ID. For example, the query IDs become ‘Query_1’, ‘Query_2’, and so on. While the hit IDs sometimes become ‘gnl|BL_ORD_ID|1’, ‘gnl|BL_ORD_ID|2’, and so on. In these cases, BLAST lumps the true sequence IDs together with their descriptions.

The blast-xml parser is aware of these modifications and will attempt to extract the true sequence IDs out of the descriptions. So when accessing QueryResult or Hit objects, you will use the non-BLAST-generated IDs.

This behavior on the query IDs can be disabled using the ‘use_raw_query_ids’ parameter while the behavior on the hit IDs can be disabled using the ‘use_raw_hit_ids’ parameter. Both are boolean values that can be supplied to SearchIO.read or SearchIO.parse, with the default values set to ‘False’.

In any case, the raw BLAST IDs can always be accessed using the query or hit object’s ‘blast_id’ attribute.

The blast-xml write function also accepts ‘use_raw_query_ids’ and ‘use_raw_hit_ids’ parameters. However, note that the default values for the writer are set to ‘True’. This is because the writer is meant to mimic native BLAST result as much as possible.

blast-tab

The default format for blast-tab support is the variant without comments (-m 6 flag). Commented BLAST tabular files may be parsed, indexed, or written using the keyword argument ‘comments’ set to True:

>>> # blast-tab defaults to parsing uncommented files
>>> from Bio import SearchIO
>>> uncommented = 'Blast/tab_2226_tblastn_004.txt'
>>> qresult = SearchIO.read(uncommented, 'blast-tab')
>>> qresult
QueryResult(id='gi|11464971:4-101', 5 hits)

>>> # set the keyword argument to parse commented files
>>> commented = 'Blast/tab_2226_tblastn_008.txt'
>>> qresult = SearchIO.read(commented, 'blast-tab', comments=True)
>>> qresult
QueryResult(id='gi|11464971:4-101', 5 hits)

For uncommented files, the parser defaults to using BLAST’s default column ordering: ‘qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore’.

If you want to parse an uncommented file with a customized column order, you can use the ‘fields’ keyword argument to pass the custom column order. The names of the column follow BLAST’s naming. For example, ‘qseqid’ is the column for the query sequence ID. These names may be passed either as a Python list or as a space-separated strings.

>>> # pass the custom column names as a Python list
>>> fname = 'Blast/tab_2226_tblastn_009.txt'
>>> custom_fields = ['qseqid', 'sseqid']
>>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
>>> qresult
QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)

>>> # pass the custom column names as a space-separated string
>>> fname = 'Blast/tab_2226_tblastn_009.txt'
>>> custom_fields = 'qseqid sseqid'
>>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
>>> qresult
QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)

You may also use the ‘std’ field name as an alias to BLAST’s default 12 columns, just like when you run a command line BLAST search.

Note that the ‘fields’ keyword argument will be ignored if the parsed file is commented. Commented files have their column ordering stated explicitly in the file, so there is no need to specify it again in SearchIO.

‘comments’ and ‘fields’ keyword arguments are both applicable for parsing, indexing, and writing.

blast-tab provides the following attributes for each SearchIO objects:

Object

Attribute

Column name

QueryResult

accession

qacc

accession_version

qaccver

gi

qgi

seq_len

qlen

id

qseqid

Hit

accession

sacc

accession_version

sacc_ver

gi

sgi

gi_all

sallgi

id_all

sallseqid

seq_len

slen

id

sseqid

HSP

bitscore

bitscore

btop

btop

evalue

evalue

gapopen_num

gapopen

gap_num

gaps

ident_num

nident

ident_pct

pident

mismatch_num

mismatch

pos_pct

ppos

pos_num

positive

bitscore_raw

score

HSPFragment (also via HSP)

frames

frames [2]

aln_span

length

query_end

qend

query_frame

qframe

query

qseq

query_start

qstart

hit_end

send

hit_frame

sframe

hit

sseq

hit_start

sstart

If the parsed file is commented, the following attributes may be available as well:

Object

Attribute

Value

QueryResult

description

query description

fields

columns in the output file

program

BLAST flavor

rid

remote search ID

target

target database

version

BLAST version