Bio.SearchIO.BlastIO.blast_xml module
Bio.SearchIO parser for BLAST+ XML output formats.
- class Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser(handle, use_raw_query_ids=False, use_raw_hit_ids=False)
Bases:
object
Parser for the BLAST XML format.
- __init__(handle, use_raw_query_ids=False, use_raw_hit_ids=False)
Initialize the class.
- __iter__()
Iterate over BlastXmlParser object yields query results.
- class Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer(filename, **kwargs)
Bases:
SearchIndexer
Indexer class for BLAST XML output.
- qstart_mark = b'<Iteration>'
- qend_mark = b'</Iteration>'
- block_size = 16384
- __init__(filename, **kwargs)
Initialize the class.
- __iter__()
Iterate over BlastXmlIndexer yields qstart_id, start_offset, block’s length.
- get_raw(offset)
Return the raw record from the file as a bytes string.
- __abstractmethods__ = frozenset({})
- class Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter(handle, use_raw_query_ids=True, use_raw_hit_ids=True)
Bases:
object
Stream-based BLAST+ XML Writer.
- __init__(handle, use_raw_query_ids=True, use_raw_hit_ids=True)
Initialize the class.
- write_file(qresults)
Write the XML contents to the output handle.