Bio.SearchIO.FastaIO module

Bio.SearchIO support for Bill Pearson’s FASTA tools.

This module adds support for parsing FASTA outputs. FASTA is a suite of programs that finds regions of local or global similarity between protein or nucleotide sequences, either by searching databases or identifying local duplications.

Bio.SearchIO.FastaIO was tested on the following FASTA flavors and versions:

• flavors: fasta, ssearch, tfastx

• versions: 35, 36

Other flavors and/or versions may introduce some bugs. Please file a bug report if you see such problems to Biopython’s bug tracker.

More information on FASTA are available through these links:

• Website: http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

• User guide: http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf

Supported Formats

Bio.SearchIO.FastaIO supports parsing and indexing FASTA outputs triggered by the -m 10 flag. Other formats that mimic other programs (e.g. the BLAST tabular format using the -m 8 flag) may be parseable but using SearchIO’s other parsers (in this case, using the ‘blast-tab’ parser).

fasta-m10

Note that in FASTA -m 10 outputs, HSPs from different strands are considered to be from different hits. They are listed as two separate entries in the hit table. FastaIO recognizes this and will group HSPs with the same hit ID into a single Hit object, regardless of strand.

FASTA also sometimes output extra sequences adjacent to the HSP match. These extra sequences are discarded by FastaIO. Only regions containing the actual sequence match are extracted.

The following object attributes are provided:

Object	Attribute	Value
QueryResult	description	query sequence description
	id	query sequence ID
	program	FASTA flavor
	seq_len	full length of query sequence
	target	target search database
	version	FASTA version
Hit	seq_len	full length of the hit sequence
HSP	bitscore	*_bits line
	evalue	*_expect line
	ident_pct	*_ident line
	init1_score	*_init1 line
	initn_score	*_initn line
	opt_score	*_opt line, *_s-w opt line
	pos_pct	*_sim line
	sw_score	*_score line
	z_score	*_z-score line
HSPFragment (also via HSP)	aln_annotation	al_cons block, if present
	hit	hit sequence
	hit_end	hit sequence end coordinate
	hit_start	hit sequence start coordinate
	hit_strand	hit sequence strand
	query	query sequence
	query_end	query sequence end coordinate
	query_start	query sequence start coordinate
	query_strand	query sequence strand

class Bio.SearchIO.FastaIO.FastaM10Parser(handle, _FastaM10Parser__parse_hit_table=False)

Bases: object

Parser for Bill Pearson’s FASTA suite’s -m 10 output.

__init__(self, handle, _FastaM10Parser__parse_hit_table=False)

Initialize the class.

__iter__(self)

Iterate over FastaM10Parser object yields query results.

class Bio.SearchIO.FastaIO.FastaM10Indexer(filename)

Bases: Bio.SearchIO._index.SearchIndexer

Indexer class for Bill Pearson’s FASTA suite’s -m 10 output.

__init__(self, filename)

Initialize the class.

__iter__(self)

Iterate over FastaM10Indexer; yields query results’ keys, start offsets, offset lengths.

get_raw(self, offset)

Return the raw record from the file as a bytes string.