Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_tab

Module blast_tab

Bio.SearchIO parser for BLAST+ tab output format, with or without comments.

Classes

[hide private]

BlastTabParser
Parser for the BLAST tabular format.

BlastTabIndexer
Indexer class for BLAST+ tab output.

BlastTabWriter
Writer for blast-tab output format.

Functions

[hide private]

_compute_gapopen_num(hsp)
Returns the number of gap openings in the given HSP.

source code

_augment_blast_hsp(hsp, attr)
Calculates the given HSP attribute, for writing.

source code

Variables

[hide private]

_LONG_SHORT_MAP = {'% identity': 'pident', '% positives': 'ppo...

_COLUMN_QRESULT = {'qacc': ('accession', <type 'str'>), 'qaccv...

_COLUMN_HIT = {'sacc': ('accession', <type 'str'>), 'saccver':...

_COLUMN_HSP = {'bitscore': ('bitscore', <type 'float'>), 'btop...

_COLUMN_FRAG = {'frames': ('frames', <type 'str'>), 'length': ...

_SUPPORTED_FIELDS = set(['bitscore', 'btop', 'evalue', 'frames...

_DEFAULT_FIELDS = ['qseqid', 'sseqid', 'pident', 'length', 'mi...

_MIN_QUERY_FIELDS = set(['qacc', 'qaccver', 'qseqid'])

_MIN_HIT_FIELDS = set(['sacc', 'saccver', 'sseqid'])

_RE_GAPOPEN = re.compile(r'\w-')

Variables Details

[hide private]

_LONG_SHORT_MAP

Value:

{'% identity': 'pident',
 '% positives': 'ppos',
 'BTOP': 'btop',
 'alignment length': 'length',
 'bit score': 'bitscore',
 'evalue': 'evalue',
 'gap opens': 'gapopen',
 'gaps': 'gaps',
...

_COLUMN_QRESULT

Value:

{'qacc': ('accession', <type 'str'>),
 'qaccver': ('accession_version', <type 'str'>),
 'qgi': ('gi', <type 'str'>),
 'qlen': ('seq_len', <type 'int'>),
 'qseqid': ('id', <type 'str'>)}

_COLUMN_HIT

Value:

{'sacc': ('accession', <type 'str'>),
 'saccver': ('accession_version', <type 'str'>),
 'sallgi': ('gi_all', <type 'str'>),
 'sallseqid': ('id_all', <type 'str'>),
 'sgi': ('gi', <type 'str'>),
 'slen': ('seq_len', <type 'int'>),
 'sseqid': ('id', <type 'str'>)}

_COLUMN_HSP

Value:

{'bitscore': ('bitscore', <type 'float'>),
 'btop': ('btop', <type 'str'>),
 'evalue': ('evalue', <type 'float'>),
 'gapopen': ('gapopen_num', <type 'int'>),
 'gaps': ('gap_num', <type 'int'>),
 'mismatch': ('mismatch_num', <type 'int'>),
 'nident': ('ident_num', <type 'int'>),
 'pident': ('ident_pct', <type 'float'>),
...

_COLUMN_FRAG

Value:

{'frames': ('frames', <type 'str'>),
 'length': ('aln_span', <type 'int'>),
 'qend': ('query_end', <type 'int'>),
 'qframe': ('query_frame', <type 'int'>),
 'qseq': ('query', <type 'str'>),
 'qstart': ('query_start', <type 'int'>),
 'send': ('hit_end', <type 'int'>),
 'sframe': ('hit_frame', <type 'int'>),
...

_SUPPORTED_FIELDS

Value:

set(['bitscore',
     'btop',
     'evalue',
     'frames',
     'gapopen',
     'gaps',
     'length',
     'mismatch',
...

_DEFAULT_FIELDS

Value:

['qseqid',
 'sseqid',
 'pident',
 'length',
 'mismatch',
 'gapopen',
 'qstart',
 'qend',
...