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.
-