Bio.SearchIO.BlastIO.blast_tab module

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

class Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer(filename, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Bases: Bio.SearchIO._index.SearchIndexer

Indexer class for BLAST+ tab output.

__init__(self, filename, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Initialize the class.

__iter__(self)

Iterate over the file handle; yields key, start offset, and length.

get_raw(self, offset)

Return the raw bytes string of a QueryResult object from the given offset.

class Bio.SearchIO.BlastIO.blast_tab.BlastTabParser(handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Bases: object

Parser for the BLAST tabular format.

__init__(self, handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Initialize the class.

__iter__(self)

Iterate over BlastTabParser, yields query results.

class Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter(handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Bases: object

Writer for blast-tab output format.

__init__(self, handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'])

Initialize the class.

write_file(self, qresults)

Write to the handle, return how many QueryResult objects were written.