# 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__(handle, _FastaM10Parser__parse_hit_table=False)

    Initialize the class.

  __iter__()

    Iterate over FastaM10Parser object yields query results.

  __firstlineno__ = 269
  __static_attributes__ = ('_preamble', 'handle', 'line')

class Bio.SearchIO.FastaIO.FastaM10Indexer(filename)

  Bases: `SearchIndexer`

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

  __init__(filename)

    Initialize the class.

  __iter__()

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

  get_raw(offset)

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

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 528
  __static_attributes__ = ()

Biopython v: 1.85

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