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=_DEFAULT_FIELDS)

Bases: SearchIndexer

Indexer class for BLAST+ tab output.

__init__(filename, comments=False, fields=_DEFAULT_FIELDS)

Initialize the class.

__iter__()

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

get_raw(offset)

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

__abstractmethods__ = frozenset({})

class Bio.SearchIO.BlastIO.blast_tab.BlastTabParser(handle, comments=False, fields=_DEFAULT_FIELDS)

Bases: object

Parser for the BLAST tabular format.

__init__(handle, comments=False, fields=_DEFAULT_FIELDS)

Initialize the class.

__iter__()

Iterate over BlastTabParser, yields query results.

class Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter(handle, comments=False, fields=_DEFAULT_FIELDS)

Bases: object

Writer for blast-tab output format.

__init__(handle, comments=False, fields=_DEFAULT_FIELDS)

Initialize the class.

write_file(qresults)

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