Bio.Blast package
Submodules
- Bio.Blast.Applications module
NcbiblastpCommandline
NcbiblastpCommandline.__init__()
NcbiblastpCommandline.best_hit_overhang
NcbiblastpCommandline.best_hit_score_edge
NcbiblastpCommandline.comp_based_stats
NcbiblastpCommandline.culling_limit
NcbiblastpCommandline.db
NcbiblastpCommandline.db_hard_mask
NcbiblastpCommandline.db_soft_mask
NcbiblastpCommandline.dbsize
NcbiblastpCommandline.entrez_query
NcbiblastpCommandline.evalue
NcbiblastpCommandline.export_search_strategy
NcbiblastpCommandline.gapextend
NcbiblastpCommandline.gapopen
NcbiblastpCommandline.gilist
NcbiblastpCommandline.h
NcbiblastpCommandline.help
NcbiblastpCommandline.html
NcbiblastpCommandline.import_search_strategy
NcbiblastpCommandline.lcase_masking
NcbiblastpCommandline.line_length
NcbiblastpCommandline.matrix
NcbiblastpCommandline.max_hsps
NcbiblastpCommandline.max_hsps_per_subject
NcbiblastpCommandline.max_target_seqs
NcbiblastpCommandline.negative_gilist
NcbiblastpCommandline.negative_seqidlist
NcbiblastpCommandline.num_alignments
NcbiblastpCommandline.num_descriptions
NcbiblastpCommandline.num_threads
NcbiblastpCommandline.out
NcbiblastpCommandline.outfmt
NcbiblastpCommandline.parse_deflines
NcbiblastpCommandline.qcov_hsp_perc
NcbiblastpCommandline.query
NcbiblastpCommandline.query_loc
NcbiblastpCommandline.remote
NcbiblastpCommandline.searchsp
NcbiblastpCommandline.seg
NcbiblastpCommandline.seqidlist
NcbiblastpCommandline.show_gis
NcbiblastpCommandline.soft_masking
NcbiblastpCommandline.subject
NcbiblastpCommandline.subject_loc
NcbiblastpCommandline.sum_statistics
NcbiblastpCommandline.sum_stats
NcbiblastpCommandline.task
NcbiblastpCommandline.threshold
NcbiblastpCommandline.ungapped
NcbiblastpCommandline.use_sw_tback
NcbiblastpCommandline.version
NcbiblastpCommandline.window_size
NcbiblastpCommandline.word_size
NcbiblastpCommandline.xdrop_gap
NcbiblastpCommandline.xdrop_gap_final
NcbiblastpCommandline.xdrop_ungap
NcbiblastnCommandline
NcbiblastnCommandline.__init__()
NcbiblastnCommandline.best_hit_overhang
NcbiblastnCommandline.best_hit_score_edge
NcbiblastnCommandline.culling_limit
NcbiblastnCommandline.db
NcbiblastnCommandline.db_hard_mask
NcbiblastnCommandline.db_soft_mask
NcbiblastnCommandline.dbsize
NcbiblastnCommandline.dust
NcbiblastnCommandline.entrez_query
NcbiblastnCommandline.evalue
NcbiblastnCommandline.export_search_strategy
NcbiblastnCommandline.filtering_db
NcbiblastnCommandline.gapextend
NcbiblastnCommandline.gapopen
NcbiblastnCommandline.gilist
NcbiblastnCommandline.h
NcbiblastnCommandline.help
NcbiblastnCommandline.html
NcbiblastnCommandline.import_search_strategy
NcbiblastnCommandline.index_name
NcbiblastnCommandline.lcase_masking
NcbiblastnCommandline.line_length
NcbiblastnCommandline.max_hsps
NcbiblastnCommandline.max_hsps_per_subject
NcbiblastnCommandline.max_target_seqs
NcbiblastnCommandline.min_raw_gapped_score
NcbiblastnCommandline.negative_gilist
NcbiblastnCommandline.negative_seqidlist
NcbiblastnCommandline.no_greedy
NcbiblastnCommandline.num_alignments
NcbiblastnCommandline.num_descriptions
NcbiblastnCommandline.num_threads
NcbiblastnCommandline.off_diagonal_range
NcbiblastnCommandline.out
NcbiblastnCommandline.outfmt
NcbiblastnCommandline.parse_deflines
NcbiblastnCommandline.penalty
NcbiblastnCommandline.perc_identity
NcbiblastnCommandline.qcov_hsp_perc
NcbiblastnCommandline.query
NcbiblastnCommandline.query_loc
NcbiblastnCommandline.remote
NcbiblastnCommandline.reward
NcbiblastnCommandline.searchsp
NcbiblastnCommandline.seqidlist
NcbiblastnCommandline.show_gis
NcbiblastnCommandline.soft_masking
NcbiblastnCommandline.strand
NcbiblastnCommandline.subject
NcbiblastnCommandline.subject_loc
NcbiblastnCommandline.sum_statistics
NcbiblastnCommandline.sum_stats
NcbiblastnCommandline.task
NcbiblastnCommandline.template_length
NcbiblastnCommandline.template_type
NcbiblastnCommandline.ungapped
NcbiblastnCommandline.use_index
NcbiblastnCommandline.version
NcbiblastnCommandline.window_masker_db
NcbiblastnCommandline.window_masker_taxid
NcbiblastnCommandline.window_size
NcbiblastnCommandline.word_size
NcbiblastnCommandline.xdrop_gap
NcbiblastnCommandline.xdrop_gap_final
NcbiblastnCommandline.xdrop_ungap
NcbiblastxCommandline
NcbiblastxCommandline.__init__()
NcbiblastxCommandline.best_hit_overhang
NcbiblastxCommandline.best_hit_score_edge
NcbiblastxCommandline.comp_based_stats
NcbiblastxCommandline.culling_limit
NcbiblastxCommandline.db
NcbiblastxCommandline.db_hard_mask
NcbiblastxCommandline.db_soft_mask
NcbiblastxCommandline.dbsize
NcbiblastxCommandline.entrez_query
NcbiblastxCommandline.evalue
NcbiblastxCommandline.export_search_strategy
NcbiblastxCommandline.frame_shift_penalty
NcbiblastxCommandline.gapextend
NcbiblastxCommandline.gapopen
NcbiblastxCommandline.gilist
NcbiblastxCommandline.h
NcbiblastxCommandline.help
NcbiblastxCommandline.html
NcbiblastxCommandline.import_search_strategy
NcbiblastxCommandline.lcase_masking
NcbiblastxCommandline.line_length
NcbiblastxCommandline.matrix
NcbiblastxCommandline.max_hsps
NcbiblastxCommandline.max_hsps_per_subject
NcbiblastxCommandline.max_intron_length
NcbiblastxCommandline.max_target_seqs
NcbiblastxCommandline.negative_gilist
NcbiblastxCommandline.negative_seqidlist
NcbiblastxCommandline.num_alignments
NcbiblastxCommandline.num_descriptions
NcbiblastxCommandline.num_threads
NcbiblastxCommandline.out
NcbiblastxCommandline.outfmt
NcbiblastxCommandline.parse_deflines
NcbiblastxCommandline.qcov_hsp_perc
NcbiblastxCommandline.query
NcbiblastxCommandline.query_gencode
NcbiblastxCommandline.query_loc
NcbiblastxCommandline.remote
NcbiblastxCommandline.searchsp
NcbiblastxCommandline.seg
NcbiblastxCommandline.seqidlist
NcbiblastxCommandline.show_gis
NcbiblastxCommandline.soft_masking
NcbiblastxCommandline.strand
NcbiblastxCommandline.subject
NcbiblastxCommandline.subject_loc
NcbiblastxCommandline.sum_statistics
NcbiblastxCommandline.sum_stats
NcbiblastxCommandline.task
NcbiblastxCommandline.threshold
NcbiblastxCommandline.ungapped
NcbiblastxCommandline.use_sw_tback
NcbiblastxCommandline.version
NcbiblastxCommandline.window_size
NcbiblastxCommandline.word_size
NcbiblastxCommandline.xdrop_gap
NcbiblastxCommandline.xdrop_gap_final
NcbiblastxCommandline.xdrop_ungap
NcbitblastnCommandline
NcbitblastnCommandline.__init__()
NcbitblastnCommandline.best_hit_overhang
NcbitblastnCommandline.best_hit_score_edge
NcbitblastnCommandline.comp_based_stats
NcbitblastnCommandline.culling_limit
NcbitblastnCommandline.db
NcbitblastnCommandline.db_gencode
NcbitblastnCommandline.db_hard_mask
NcbitblastnCommandline.db_soft_mask
NcbitblastnCommandline.dbsize
NcbitblastnCommandline.entrez_query
NcbitblastnCommandline.evalue
NcbitblastnCommandline.export_search_strategy
NcbitblastnCommandline.frame_shift_penalty
NcbitblastnCommandline.gapextend
NcbitblastnCommandline.gapopen
NcbitblastnCommandline.gilist
NcbitblastnCommandline.h
NcbitblastnCommandline.help
NcbitblastnCommandline.html
NcbitblastnCommandline.import_search_strategy
NcbitblastnCommandline.in_pssm
NcbitblastnCommandline.lcase_masking
NcbitblastnCommandline.line_length
NcbitblastnCommandline.matrix
NcbitblastnCommandline.max_hsps
NcbitblastnCommandline.max_hsps_per_subject
NcbitblastnCommandline.max_intron_length
NcbitblastnCommandline.max_target_seqs
NcbitblastnCommandline.negative_gilist
NcbitblastnCommandline.negative_seqidlist
NcbitblastnCommandline.num_alignments
NcbitblastnCommandline.num_descriptions
NcbitblastnCommandline.num_threads
NcbitblastnCommandline.out
NcbitblastnCommandline.outfmt
NcbitblastnCommandline.parse_deflines
NcbitblastnCommandline.qcov_hsp_perc
NcbitblastnCommandline.query
NcbitblastnCommandline.query_loc
NcbitblastnCommandline.remote
NcbitblastnCommandline.searchsp
NcbitblastnCommandline.seg
NcbitblastnCommandline.seqidlist
NcbitblastnCommandline.show_gis
NcbitblastnCommandline.soft_masking
NcbitblastnCommandline.subject
NcbitblastnCommandline.subject_loc
NcbitblastnCommandline.sum_statistics
NcbitblastnCommandline.sum_stats
NcbitblastnCommandline.task
NcbitblastnCommandline.threshold
NcbitblastnCommandline.ungapped
NcbitblastnCommandline.use_sw_tback
NcbitblastnCommandline.version
NcbitblastnCommandline.window_size
NcbitblastnCommandline.word_size
NcbitblastnCommandline.xdrop_gap
NcbitblastnCommandline.xdrop_gap_final
NcbitblastnCommandline.xdrop_ungap
NcbitblastxCommandline
NcbitblastxCommandline.__init__()
NcbitblastxCommandline.best_hit_overhang
NcbitblastxCommandline.best_hit_score_edge
NcbitblastxCommandline.culling_limit
NcbitblastxCommandline.db
NcbitblastxCommandline.db_gencode
NcbitblastxCommandline.db_hard_mask
NcbitblastxCommandline.db_soft_mask
NcbitblastxCommandline.dbsize
NcbitblastxCommandline.entrez_query
NcbitblastxCommandline.evalue
NcbitblastxCommandline.export_search_strategy
NcbitblastxCommandline.gapextend
NcbitblastxCommandline.gapopen
NcbitblastxCommandline.gilist
NcbitblastxCommandline.h
NcbitblastxCommandline.help
NcbitblastxCommandline.html
NcbitblastxCommandline.import_search_strategy
NcbitblastxCommandline.lcase_masking
NcbitblastxCommandline.line_length
NcbitblastxCommandline.matrix
NcbitblastxCommandline.max_hsps
NcbitblastxCommandline.max_hsps_per_subject
NcbitblastxCommandline.max_intron_length
NcbitblastxCommandline.max_target_seqs
NcbitblastxCommandline.negative_gilist
NcbitblastxCommandline.negative_seqidlist
NcbitblastxCommandline.num_alignments
NcbitblastxCommandline.num_descriptions
NcbitblastxCommandline.num_threads
NcbitblastxCommandline.out
NcbitblastxCommandline.outfmt
NcbitblastxCommandline.parse_deflines
NcbitblastxCommandline.qcov_hsp_perc
NcbitblastxCommandline.query
NcbitblastxCommandline.query_gencode
NcbitblastxCommandline.query_loc
NcbitblastxCommandline.remote
NcbitblastxCommandline.searchsp
NcbitblastxCommandline.seg
NcbitblastxCommandline.seqidlist
NcbitblastxCommandline.show_gis
NcbitblastxCommandline.soft_masking
NcbitblastxCommandline.strand
NcbitblastxCommandline.subject
NcbitblastxCommandline.subject_loc
NcbitblastxCommandline.sum_statistics
NcbitblastxCommandline.sum_stats
NcbitblastxCommandline.threshold
NcbitblastxCommandline.version
NcbitblastxCommandline.window_size
NcbitblastxCommandline.word_size
NcbitblastxCommandline.xdrop_gap
NcbitblastxCommandline.xdrop_gap_final
NcbitblastxCommandline.xdrop_ungap
NcbipsiblastCommandline
NcbipsiblastCommandline.__init__()
NcbipsiblastCommandline.best_hit_overhang
NcbipsiblastCommandline.best_hit_score_edge
NcbipsiblastCommandline.comp_based_stats
NcbipsiblastCommandline.culling_limit
NcbipsiblastCommandline.db
NcbipsiblastCommandline.dbsize
NcbipsiblastCommandline.entrez_query
NcbipsiblastCommandline.evalue
NcbipsiblastCommandline.export_search_strategy
NcbipsiblastCommandline.gap_trigger
NcbipsiblastCommandline.gapextend
NcbipsiblastCommandline.gapopen
NcbipsiblastCommandline.gilist
NcbipsiblastCommandline.h
NcbipsiblastCommandline.help
NcbipsiblastCommandline.html
NcbipsiblastCommandline.ignore_msa_master
NcbipsiblastCommandline.import_search_strategy
NcbipsiblastCommandline.in_msa
NcbipsiblastCommandline.in_pssm
NcbipsiblastCommandline.inclusion_ethresh
NcbipsiblastCommandline.lcase_masking
NcbipsiblastCommandline.line_length
NcbipsiblastCommandline.matrix
NcbipsiblastCommandline.max_hsps
NcbipsiblastCommandline.max_hsps_per_subject
NcbipsiblastCommandline.max_target_seqs
NcbipsiblastCommandline.msa_master_idx
NcbipsiblastCommandline.negative_gilist
NcbipsiblastCommandline.negative_seqidlist
NcbipsiblastCommandline.num_alignments
NcbipsiblastCommandline.num_descriptions
NcbipsiblastCommandline.num_iterations
NcbipsiblastCommandline.num_threads
NcbipsiblastCommandline.out
NcbipsiblastCommandline.out_ascii_pssm
NcbipsiblastCommandline.out_pssm
NcbipsiblastCommandline.outfmt
NcbipsiblastCommandline.parse_deflines
NcbipsiblastCommandline.phi_pattern
NcbipsiblastCommandline.pseudocount
NcbipsiblastCommandline.qcov_hsp_perc
NcbipsiblastCommandline.query
NcbipsiblastCommandline.query_loc
NcbipsiblastCommandline.remote
NcbipsiblastCommandline.save_each_pssm
NcbipsiblastCommandline.save_pssm_after_last_round
NcbipsiblastCommandline.searchsp
NcbipsiblastCommandline.seg
NcbipsiblastCommandline.seqidlist
NcbipsiblastCommandline.show_gis
NcbipsiblastCommandline.soft_masking
NcbipsiblastCommandline.subject
NcbipsiblastCommandline.subject_loc
NcbipsiblastCommandline.sum_statistics
NcbipsiblastCommandline.sum_stats
NcbipsiblastCommandline.threshold
NcbipsiblastCommandline.use_sw_tback
NcbipsiblastCommandline.version
NcbipsiblastCommandline.window_size
NcbipsiblastCommandline.word_size
NcbipsiblastCommandline.xdrop_gap
NcbipsiblastCommandline.xdrop_gap_final
NcbipsiblastCommandline.xdrop_ungap
NcbirpsblastCommandline
NcbirpsblastCommandline.__init__()
NcbirpsblastCommandline.best_hit_overhang
NcbirpsblastCommandline.best_hit_score_edge
NcbirpsblastCommandline.comp_based_stats
NcbirpsblastCommandline.culling_limit
NcbirpsblastCommandline.db
NcbirpsblastCommandline.dbsize
NcbirpsblastCommandline.entrez_query
NcbirpsblastCommandline.evalue
NcbirpsblastCommandline.export_search_strategy
NcbirpsblastCommandline.gilist
NcbirpsblastCommandline.h
NcbirpsblastCommandline.help
NcbirpsblastCommandline.html
NcbirpsblastCommandline.import_search_strategy
NcbirpsblastCommandline.lcase_masking
NcbirpsblastCommandline.line_length
NcbirpsblastCommandline.max_hsps
NcbirpsblastCommandline.max_hsps_per_subject
NcbirpsblastCommandline.max_target_seqs
NcbirpsblastCommandline.negative_gilist
NcbirpsblastCommandline.negative_seqidlist
NcbirpsblastCommandline.num_alignments
NcbirpsblastCommandline.num_descriptions
NcbirpsblastCommandline.num_threads
NcbirpsblastCommandline.out
NcbirpsblastCommandline.outfmt
NcbirpsblastCommandline.parse_deflines
NcbirpsblastCommandline.qcov_hsp_perc
NcbirpsblastCommandline.query
NcbirpsblastCommandline.query_loc
NcbirpsblastCommandline.remote
NcbirpsblastCommandline.searchsp
NcbirpsblastCommandline.seg
NcbirpsblastCommandline.seqidlist
NcbirpsblastCommandline.show_gis
NcbirpsblastCommandline.soft_masking
NcbirpsblastCommandline.sum_statistics
NcbirpsblastCommandline.sum_stats
NcbirpsblastCommandline.use_sw_tback
NcbirpsblastCommandline.version
NcbirpsblastCommandline.window_size
NcbirpsblastCommandline.word_size
NcbirpsblastCommandline.xdrop_gap
NcbirpsblastCommandline.xdrop_gap_final
NcbirpsblastCommandline.xdrop_ungap
NcbirpstblastnCommandline
NcbirpstblastnCommandline.__init__()
NcbirpstblastnCommandline.comp_based_stats
NcbirpstblastnCommandline.db
NcbirpstblastnCommandline.dbsize
NcbirpstblastnCommandline.entrez_query
NcbirpstblastnCommandline.evalue
NcbirpstblastnCommandline.export_search_strategy
NcbirpstblastnCommandline.gilist
NcbirpstblastnCommandline.h
NcbirpstblastnCommandline.help
NcbirpstblastnCommandline.html
NcbirpstblastnCommandline.import_search_strategy
NcbirpstblastnCommandline.lcase_masking
NcbirpstblastnCommandline.line_length
NcbirpstblastnCommandline.max_hsps
NcbirpstblastnCommandline.max_hsps_per_subject
NcbirpstblastnCommandline.max_target_seqs
NcbirpstblastnCommandline.negative_gilist
NcbirpstblastnCommandline.negative_seqidlist
NcbirpstblastnCommandline.num_alignments
NcbirpstblastnCommandline.num_descriptions
NcbirpstblastnCommandline.num_threads
NcbirpstblastnCommandline.out
NcbirpstblastnCommandline.outfmt
NcbirpstblastnCommandline.parse_deflines
NcbirpstblastnCommandline.qcov_hsp_perc
NcbirpstblastnCommandline.query
NcbirpstblastnCommandline.query_gencode
NcbirpstblastnCommandline.query_loc
NcbirpstblastnCommandline.remote
NcbirpstblastnCommandline.searchsp
NcbirpstblastnCommandline.seg
NcbirpstblastnCommandline.seqidlist
NcbirpstblastnCommandline.show_gis
NcbirpstblastnCommandline.soft_masking
NcbirpstblastnCommandline.strand
NcbirpstblastnCommandline.sum_statistics
NcbirpstblastnCommandline.sum_stats
NcbirpstblastnCommandline.ungapped
NcbirpstblastnCommandline.use_sw_tback
NcbirpstblastnCommandline.version
NcbirpstblastnCommandline.window_size
NcbirpstblastnCommandline.word_size
NcbirpstblastnCommandline.xdrop_gap
NcbirpstblastnCommandline.xdrop_gap_final
NcbirpstblastnCommandline.xdrop_ungap
NcbiblastformatterCommandline
NcbiblastformatterCommandline.__init__()
NcbiblastformatterCommandline.archive
NcbiblastformatterCommandline.h
NcbiblastformatterCommandline.help
NcbiblastformatterCommandline.html
NcbiblastformatterCommandline.line_length
NcbiblastformatterCommandline.max_target_seqs
NcbiblastformatterCommandline.num_alignments
NcbiblastformatterCommandline.num_descriptions
NcbiblastformatterCommandline.out
NcbiblastformatterCommandline.outfmt
NcbiblastformatterCommandline.parse_deflines
NcbiblastformatterCommandline.rid
NcbiblastformatterCommandline.show_gis
NcbiblastformatterCommandline.version
NcbideltablastCommandline
NcbideltablastCommandline.__init__()
NcbideltablastCommandline.best_hit_overhang
NcbideltablastCommandline.best_hit_score_edge
NcbideltablastCommandline.comp_based_stats
NcbideltablastCommandline.culling_limit
NcbideltablastCommandline.db
NcbideltablastCommandline.dbsize
NcbideltablastCommandline.domain_inclusion_ethresh
NcbideltablastCommandline.entrez_query
NcbideltablastCommandline.evalue
NcbideltablastCommandline.export_search_strategy
NcbideltablastCommandline.gap_trigger
NcbideltablastCommandline.gapextend
NcbideltablastCommandline.gapopen
NcbideltablastCommandline.gilist
NcbideltablastCommandline.h
NcbideltablastCommandline.help
NcbideltablastCommandline.html
NcbideltablastCommandline.import_search_strategy
NcbideltablastCommandline.inclusion_ethresh
NcbideltablastCommandline.lcase_masking
NcbideltablastCommandline.line_length
NcbideltablastCommandline.matrix
NcbideltablastCommandline.max_hsps
NcbideltablastCommandline.max_hsps_per_subject
NcbideltablastCommandline.max_target_seqs
NcbideltablastCommandline.negative_gilist
NcbideltablastCommandline.negative_seqidlist
NcbideltablastCommandline.num_alignments
NcbideltablastCommandline.num_descriptions
NcbideltablastCommandline.num_iterations
NcbideltablastCommandline.num_threads
NcbideltablastCommandline.out
NcbideltablastCommandline.out_ascii_pssm
NcbideltablastCommandline.out_pssm
NcbideltablastCommandline.outfmt
NcbideltablastCommandline.parse_deflines
NcbideltablastCommandline.pseudocount
NcbideltablastCommandline.qcov_hsp_perc
NcbideltablastCommandline.query
NcbideltablastCommandline.query_loc
NcbideltablastCommandline.remote
NcbideltablastCommandline.rpsdb
NcbideltablastCommandline.save_each_pssm
NcbideltablastCommandline.save_pssm_after_last_round
NcbideltablastCommandline.searchsp
NcbideltablastCommandline.seg
NcbideltablastCommandline.seqidlist
NcbideltablastCommandline.show_domain_hits
NcbideltablastCommandline.show_gis
NcbideltablastCommandline.soft_masking
NcbideltablastCommandline.subject
NcbideltablastCommandline.subject_loc
NcbideltablastCommandline.sum_statistics
NcbideltablastCommandline.sum_stats
NcbideltablastCommandline.threshold
NcbideltablastCommandline.use_sw_tback
NcbideltablastCommandline.version
NcbideltablastCommandline.window_size
NcbideltablastCommandline.word_size
NcbideltablastCommandline.xdrop_gap
NcbideltablastCommandline.xdrop_gap_final
NcbideltablastCommandline.xdrop_ungap
NcbimakeblastdbCommandline
NcbimakeblastdbCommandline.__init__()
NcbimakeblastdbCommandline.blastdb_version
NcbimakeblastdbCommandline.dbtype
NcbimakeblastdbCommandline.gi_mask
NcbimakeblastdbCommandline.gi_mask_name
NcbimakeblastdbCommandline.h
NcbimakeblastdbCommandline.hash_index
NcbimakeblastdbCommandline.help
NcbimakeblastdbCommandline.input_file
NcbimakeblastdbCommandline.input_type
NcbimakeblastdbCommandline.logfile
NcbimakeblastdbCommandline.mask_data
NcbimakeblastdbCommandline.mask_desc
NcbimakeblastdbCommandline.mask_id
NcbimakeblastdbCommandline.max_file_sz
NcbimakeblastdbCommandline.out
NcbimakeblastdbCommandline.parse_seqids
NcbimakeblastdbCommandline.taxid
NcbimakeblastdbCommandline.taxid_map
NcbimakeblastdbCommandline.title
NcbimakeblastdbCommandline.version
- Bio.Blast.NCBIWWW module
- Bio.Blast.NCBIXML module
Module contents
Code to parse and store BLAST XML output, and to invoke the NCBI BLAST web server.
This module provides code to parse and store BLAST XML output, following its definition in the associated BLAST XML DTD file: https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
This module also provides code to invoke the BLAST web server provided by NCBI. https://blast.ncbi.nlm.nih.gov/
Variables:
email Set the Blast email parameter (default is None).
tool Set the Blast tool parameter (default is
biopython
).
- exception Bio.Blast.NotXMLError(message)
Bases:
ValueError
Failed to parse file as XML.
- __init__(message)
Initialize the class.
- __str__()
Return a string summary of the exception.
- exception Bio.Blast.CorruptedXMLError(message)
Bases:
ValueError
Corrupted XML.
- __init__(message)
Initialize the class.
- __str__()
Return a string summary of the exception.
- class Bio.Blast.HSP(sequences, coordinates=None)
Bases:
Alignment
Stores an alignment of one query sequence against a target sequence.
An HSP (High-scoring Segment Pair) stores the alignment of one query sequence segment against one target (hit) sequence segment. The
Bio.Blast.HSP
class inherits from theBio.Align.Alignment
class.In addition to the
target
andquery
attributes of aBio.Align.Alignment
, aBio.Blast.HSP
object has the following attributes:score: score of HSP;
- annotations: a dictionary that may contain the following keys:
‘bit score’: score (in bits) of HSP (float);
‘evalue’: e-value of HSP (float);
‘identity’: number of identities in HSP (integer);
‘positive’: number of positives in HSP (integer);
‘gaps’: number of gaps in HSP (integer);
‘midline’: formatting middle line.
A
Bio.Blast.HSP
object behaves the same as a Bio.Align.Alignment` object and can be used as such. However, when printing aBio.Blast.HSP
object, the BLAST e-value and bit score are included in the output (in addition to the alignment itself).See the documentation of
Bio.Blast.Record
for a more detailed explanation of how the information in BLAST records is stored in Biopython.- __repr__()
Return a representation of the alignment, including its shape.
The representation cannot be used with eval() to recreate the object, which is usually possible with simple python objects. For example:
<Alignment object (2 rows x 14 columns) at 0x10403d850>
The hex string is the memory address of the object and can be used to distinguish different Alignment objects. See help(id) for more information.
>>> import numpy as np >>> from Bio.Align import Alignment >>> alignment = Alignment(("ACCGT", "ACGT"), ... coordinates = np.array([[0, 2, 3, 5], ... [0, 2, 2, 4], ... ])) >>> print(alignment) target 0 ACCGT 5 0 ||-|| 5 query 0 AC-GT 4 >>> alignment <Alignment object (2 rows x 5 columns) at 0x...>
- __str__()
Return a human-readable string representation of the alignment.
For sequence alignments, each line has at most 80 columns. The first 10 columns show the (possibly truncated) sequence name, which may be the id attribute of a SeqRecord, or otherwise ‘target’ or ‘query’ for pairwise alignments. The next 10 columns show the sequence coordinate, using zero-based counting as usual in Python. The remaining 60 columns shown the sequence, using dashes to represent gaps. At the end of the alignment, the end coordinates are shown on the right of the sequence, again in zero-based coordinates.
Pairwise alignments have an additional line between the two sequences showing whether the sequences match (‘|’) or mismatch (‘.’), or if there is a gap (‘-‘). The coordinates shown for this line are the column indices, which can be useful when extracting a subalignment.
For example,
>>> from Bio.Align import PairwiseAligner >>> aligner = PairwiseAligner()
>>> seqA = "TTAACCCCATTTG" >>> seqB = "AAGCCCCTTT" >>> seqC = "AAAGGGGCTT"
>>> alignments = aligner.align(seqA, seqB) >>> len(alignments) 1 >>> alignment = alignments[0] >>> print(alignment) target 0 TTAA-CCCCATTTG 13 0 --||-||||-|||- 14 query 0 --AAGCCCC-TTT- 10
Note that seqC is the reverse complement of seqB. Aligning it to the reverse strand gives the same alignment, but the query coordinates are switched:
>>> alignments = aligner.align(seqA, seqC, strand="-") >>> len(alignments) 1 >>> alignment = alignments[0] >>> print(alignment) target 0 TTAA-CCCCATTTG 13 0 --||-||||-|||- 14 query 10 --AAGCCCC-TTT- 0
- class Bio.Blast.Hit(alignments=())
Bases:
Alignments
Stores a single BLAST hit of one single query against one target.
The
Bio.Blast.Hit
class inherits from theBio.Align.Alignments
class, which is a subclass of a Python list. TheBio.Blast.Hit
class storesBio.Blast.HSP
objwcts, which inherit fromBio.Align.Alignment
. ABio.Blast.Hit
object is therefore effectively a list ofBio.Align.Alignment
objects. Most hits consist of only 1 or a few Alignment objects.Each
Bio.Blast.Hit
object has atarget
attribute containing the following information:target.id: seqId of subject;
target.description: definition line of subject;
target.name: accession of subject;
len(target.seq): sequence length of subject.
See the documentation of
Bio.Blast.Record
for a more detailed explanation of the information stored in the alignments contained in theBio.Blast.Hit
object.- __getitem__(key)
x.__getitem__(y) <==> x[y]
- __repr__()
Return repr(self).
- __str__()
Return a human readable summary of the Hit object.
- __abstractmethods__ = frozenset({})
- class Bio.Blast.Record
Bases:
list
Stores the BLAST results for a single query.
A
Bio.Blast.Record
object is a list ofBio.Blast.Hit
objects, each corresponding to one hit for the query in the BLAST output.- The
Bio.Blast.Record
object may have the following attributes: - query: A
SeqRecord
object which may contain some or all of the - following information:
query.id: SeqId of query;
query.description: Definition line of query;
len(query.seq): Length of the query sequence.
- query: A
- stat: A dictionary with summary statistics of the BLAST run. It may
- contain the following keys:
‘db-num’: number of sequences in BLAST db (integer);
‘db-len’: length of BLAST db (integer);
‘hsp-len’: effective HSP length (integer);
‘eff-space’: effective search space (float);
‘kappa’: Karlin-Altschul parameter K (float);
‘lambda’: Karlin-Altschul parameter Lambda (float);
‘entropy’: Karlin-Altschul parameter H (float).
message: Some (error?) information.
Each
Bio.Blast.Hit
object has atarget
attribute containing the following information:target.id: seqId of subject;
target.description: definition line of subject;
target.name: accession of subject;
len(target.seq): sequence length of subject.
The
Bio.Blast.Hit
class inherits from theBio.Align.Alignments
class, which inherits from a Python list. In this list, theBio.Blast.Hit
object storesBio.Blast.HSP
objects, which inherit from theBio.Align.Alignment
class. ABio.Blast.Hit
object is therefore effectively a list of alignment objects.Each HSP in a
Bio.Blast.Hit
object has the attributestarget
andquery
attributes, as usual for of aBio.Align.Alignment
object storing a pairwise alignment, pointing to aSeqRecord
object representing the target and query, respectively. For translated BLAST searches, thefeatures
attribute of the target or query may contain aSeqFeature
of type CDS that stores the amino acid sequence region. Thequalifiers
attribute of such a feature is a dictionary with a single key ‘coded_by’; the corresponding value specifies the nucleotide sequence region, in a GenBank-style string with 1-based coordinates, that encodes the amino acid sequence.Each
Bio.Blast.HSP
object has the following additional attributes:score: score of HSP;
- annotations: a dictionary that may contain the following keys:
‘bit score’: score (in bits) of HSP (float);
‘evalue’: e-value of HSP (float);
‘identity’: number of identities in HSP (integer);
‘positive’: number of positives in HSP (integer);
‘gaps’: number of gaps in HSP (integer);
‘midline’: formatting middle line.
>>> from Bio import Blast >>> record = Blast.read("Blast/xml_2212L_blastx_001.xml") >>> record.query SeqRecord(seq=Seq(None, length=556), id='gi|1347369|gb|G25137.1|G25137', name='<unknown name>', description='human STS EST48004, sequence tagged site', dbxrefs=[]) >>> record.stat {'db-num': 2934173, 'db-len': 1011751523, 'hsp-len': 0, 'eff-space': 0, 'kappa': 0.041, 'lambda': 0.267, 'entropy': 0.14} >>> len(record) 78 >>> hit = record[0] >>> type(hit) <class 'Bio.Blast.Hit'> >>> from Bio.Align import Alignments >>> isinstance(hit, Alignments) True >>> hit.target SeqRecord(seq=Seq(None, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[])
Most hits consist of only 1 or a few Alignment objects:
>>> len(hit) 1 >>> alignment = hit[0] >>> type(alignment) <class 'Bio.Blast.HSP'> >>> alignment.score 630.0 >>> alignment.annotations {'bit score': 247.284, 'evalue': 1.69599e-64, 'identity': 122, 'positive': 123, 'gaps': 0, 'midline': 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+'}
Target and query information are stored in the respective attributes of the alignment:
>>> alignment.target SeqRecord(seq=Seq({155: 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...TKK'}, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[]) >>> alignment.query SeqRecord(seq=Seq('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...XKE'), id='gi|1347369|gb|G25137.1|G25137', name='<unknown name>', description='human STS EST48004, sequence tagged site', dbxrefs=[])
This was a BLASTX run, so the query sequence was translated:
>>> len(alignment.target.features) 0 >>> len(alignment.query.features) 1 >>> feature = alignment.query.features[0] >>> feature SeqFeature(SimpleLocation(ExactPosition(0), ExactPosition(133)), type='CDS', qualifiers=...) >>> feature.qualifiers {'coded_by': 'gi|1347369|gb|G25137.1|G25137:1..399'}
i.e., nucleotides 0:399 (in zero-based coordinates) encode the amino acids of the query in the alignment.
For an alignment against the reverse strand, the location in the qualifier is shown as in this example:
>>> record[72][0].query.features[0].qualifiers {'coded_by': 'complement(gi|1347369|gb|G25137.1|G25137:345..530)'}
- __init__()
Initialize the Record object.
- __repr__()
Return repr(self).
- __str__()
Return str(self).
- __getitem__(key)
x.__getitem__(y) <==> x[y]
- keys()
Return a list of the target.id of each hit.
- __contains__(key)
Return key in self.
- index(key)
Return the index of the hit for which the target.id is equal to the key.
- The
- class Bio.Blast.Records(source)
Bases:
UserList
Stores the BLAST results of a single BLAST run.
A
Bio.Blast.Records
object is an iterator. Iterating over it returns returnsBio.Blast.Record
objects, each of which corresponds to one BLAST query.Common attributes of a
Bio.Blast.Records
object are- source: The input data from which the
Bio.Blast.Records
object was constructed.
- source: The input data from which the
program: The specific BLAST program that was used (e.g., ‘blastn’).
version: The version of the BLAST program (e.g., ‘BLASTN 2.2.27+’).
reference: The literature reference to the BLAST publication.
- db: The BLAST database against which the query was run
(e.g., ‘nr’).
- query: A
SeqRecord
object which may contain some or all of the - following information:
query.id: SeqId of the query;
query.description: Definition line of the query;
- query.seq: The query sequence. The query sequence.
The query sequence.
- query: A
- param: A dictionary with the parameters used for the BLAST run.
- You may find the following keys in this dictionary:
- ‘matrix’: the scoring matrix used in the BLAST run
(e.g., ‘BLOSUM62’) (string);
- ‘expect’: threshold on the expected number of chance
matches (float);
- ‘include’: e-value threshold for inclusion in
multipass model in psiblast (float);
‘sc-match’: score for matching nucleotides (integer);
- ‘sc-mismatch’: score for mismatched nucleotides
(integer);
‘gap-open’: gap opening cost (integer);
‘gap-extend’: gap extension cost (integer);
- ‘filter’: filtering options applied in the BLAST
run (string);
‘pattern’: PHI-BLAST pattern (string);
‘entrez-query’: Limit of request to Entrez query (string).
- mbstat: A dictionary with Mega BLAST search statistics. As this
information is stored near the end of the XML file, this attribute can only be accessed after the file has been read completely (by iterating over the records until a
StopIteration
is issued. This dictionary can contain the same keys as the dictionary stored under thestat
attribute of aRecord
object.
>>> from Bio import Blast >>> path = "Blast/xml_2218_blastp_002.xml"
In a script, you would use a
with
block, as in>>> with Blast.parse(path) as records: ... print(records.source) ... Blast/xml_2218_blastp_002.xml
to ensure that the file is closed at the end of the block. Here, we will simply do
>>> records = Blast.parse("Blast/xml_2218_blastp_002.xml")
so we can see the output of each command right away.
>>> type(records) <class 'Bio.Blast.Records'> >>> records.source 'Blast/xml_2218_blastp_002.xml' >>> records.program 'blastp' >>> records.version 'BLASTP 2.2.18+' >>> records.reference 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.' >>> records.db 'gpipe/9606/Previous/protein' >>> records.param {'matrix': 'BLOSUM62', 'expect': 0.01, 'gap-open': 11, 'gap-extend': 1, 'filter': 'm L; R -d repeat/repeat_9606;'}
Iterating over the records returns Bio.Blast.Record objects:
>>> record = next(records) >>> type(record) <class 'Bio.Blast.Record'> >>> record.query.id 'gi|585505|sp|Q08386|MOPB_RHOCA' >>> record = next(records) >>> type(record) <class 'Bio.Blast.Record'> >>> record.query.id 'gi|129628|sp|P07175.1|PARA_AGRTU' >>> record = next(records) Traceback (most recent call last): ... StopIteration
You can also use the records as a list, for example by extracting a record by index, or by calling
len
orprint
on the records. The parser will then automatically iterate over the records and store them:>>> records = Blast.parse("Blast/wnts.xml") >>> record = records[3] # this causes all records to be read in and stored >>> record.query.id 'Query_4' >>> len(records) 5
After the records have been read in, you can still iterate over them:
>>> for i, record in enumerate(records): ... print(i, record.query.id) ... 0 Query_1 1 Query_2 2 Query_3 3 Query_4 4 Query_5
- __init__(source)
Initialize the Records object.
- __enter__()
- __exit__(exc_type, exc_value, exc_traceback)
- __iter__()
- __next__()
- __getitem__(index)
- property data
Overrides the data attribute of UserList.
- __repr__()
Return repr(self).
- __str__()
Return str(self).
- __abstractmethods__ = frozenset({})
- Bio.Blast.parse(source)
Parse an XML file containing BLAST output and return a Bio.Blast.Records object.
This returns an iterator object; iterating over it returns Bio.Blast.Record objects one by one.
The source can be a file stream or the path to an XML file containing the BLAST output. If a file stream, source must be in binary mode. This allows the parser to detect the encoding from the XML file,and to use it to convert any text in the XML to the correct Unicode string. The qblast function in Bio.Blast returns a file stream in binary mode. For files, please use mode “rb” when opening the file, as in
>>> from Bio import Blast >>> stream = open("Blast/wnts.xml", "rb") # opened in binary mode >>> records = Blast.parse(stream) >>> for record in records: ... print(record.query.id, record.query.description) ... Query_1 gi|195230749:301-1383 Homo sapiens wingless-type MMTV integration site family member 2 (WNT2), transcript variant 1, mRNA Query_2 gi|325053704:108-1166 Homo sapiens wingless-type MMTV integration site family, member 3A (WNT3A), mRNA Query_3 gi|156630997:105-1160 Homo sapiens wingless-type MMTV integration site family, member 4 (WNT4), mRNA Query_4 gi|371502086:108-1205 Homo sapiens wingless-type MMTV integration site family, member 5A (WNT5A), transcript variant 2, mRNA Query_5 gi|53729353:216-1313 Homo sapiens wingless-type MMTV integration site family, member 6 (WNT6), mRNA >>> stream.close()
- Bio.Blast.read(source)
Parse an XML file containing BLAST output for a single query and return it.
Internally, this function uses Bio.Blast.parse to obtain an iterator over BLAST records. The function then reads one record from the iterator, ensures that there are no further records, and returns the record it found as a Bio.Blast.Record object. An exception is raised if no records are found, or more than one record is found.
The source can be a file stream or the path to an XML file containing the BLAST output. If a file stream, source must be in binary mode. This allows the parser to detect the encoding from the XML file,and to use it to convert any text in the XML to the correct Unicode string. The qblast function in Bio.Blast returns a file stream in binary mode. For files, please use mode “rb” when opening the file, as in
>>> from Bio import Blast >>> stream = open("Blast/xml_21500_blastn_001.xml", "rb") # opened in binary mode >>> record = Blast.read(stream) >>> record.query.id 'Query_78041' >>> record.query.description 'G26684.1 human STS STS_D11570, sequence tagged site' >>> len(record) 11 >>> stream.close()
Use the Bio.Blast.parse function if you want to read a file containing BLAST output for more than one query.
- Bio.Blast.write(records, destination, fmt='XML')
Write BLAST records as an XML file, and return the number of records.
- Arguments:
records - A
Bio.Blast.Records
object.- destination - File or file-like object to write to, or filename as
string. The File object must have been opened for writing in binary mode, and must be closed (or flushed) by the caller after this function returns to ensure that all records are written.
- fmt - string describing the file format to write
(case-insensitive). Currently, only “XML” and “XML2” are accepted.
Returns the number of records written (as an integer).
- Bio.Blast.qblast(program, database, sequence, url_base=NCBI_BLAST_URL, auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, short_query=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None, template_type=None, template_length=None, username='blast', password=None)
BLAST search using NCBI’s QBLAST server.
Supports all parameters of the old qblast API for Put and Get.
Please note that NCBI uses the new Common URL API for BLAST searches on the internet (https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html). Thus, some of the parameters used by this function are not (or are no longer) officially supported by NCBI. Although they are still functioning, this may change in the future.
Some useful parameters:
program blastn, blastp, blastx, tblastn, or tblastx (lower case)
database Which database to search against (e.g. “nr”).
sequence The sequence to search.
ncbi_gi TRUE/FALSE whether to give ‘gi’ identifier.
descriptions Number of descriptions to show. Def 500.
alignments Number of alignments to show. Def 500.
expect An expect value cutoff. Def 10.0.
matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
filter “none” turns off filtering. Default no filtering
- format_type “XML” (default), “HTML”, “Text”, “XML2”, “JSON2”,
or “Tabular”.
entrez_query Entrez query to limit Blast search - only applies when searching nucleotide BLASTDBs
hitlist_size Number of hits to return. Default 50
megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- short_query TRUE/FALSE whether to adjust the search parameters for a
short query sequence. Note that this will override manually set parameters like word size and e value. Turns off when sequence length is > 30 residues. Default: None.
service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters and passes the values to the server as is. More help is available at: https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html
The http.client.HTTPResponse object returned by this function has the additional attributes rid and rtoe with the Request ID and Request Time Of Execution for this BLAST search.