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