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.