Bio.SearchIO.HmmerIO.hmmer2_text module¶
Bio.SearchIO parser for HMMER 2 text output.
-
class
Bio.SearchIO.HmmerIO.hmmer2_text.
Hmmer2TextParser
(handle)¶ Bases:
object
Iterator for the HMMER 2.0 text output.
-
__init__
(self, handle)¶ Initialize the class.
-
__iter__
(self)¶ Iterate over Hmmer2TextParser, yields query results.
-
read_next
(self, rstrip=True)¶ Return the next non-empty line, trailing whitespace removed.
-
push_back
(self, line)¶ Un-read a line that should not be parsed yet.
-
parse_key_value
(self)¶ Parse key-value pair separated by colon.
-
parse_preamble
(self)¶ Parse HMMER2 preamble.
-
parse_qresult
(self)¶ Parse a HMMER2 query block.
-
parse_hits
(self)¶ Parse a HMMER2 hit block, beginning with the hit table.
-
parse_hsps
(self, hit_placeholders)¶ Parse a HMMER2 hsp block, beginning with the hsp table.
-
parse_hsp_alignments
(self)¶ Parse a HMMER2 HSP alignment block.
-
-
class
Bio.SearchIO.HmmerIO.hmmer2_text.
Hmmer2TextIndexer
(*args, **kwargs)¶ Bases:
Bio.SearchIO.HmmerIO._base._BaseHmmerTextIndexer
Indexer for hmmer2-text format.
-
qresult_start
= b'Query'¶
-
qresult_end
= b'//'¶
-
__iter__
(self)¶ Iterate over Hmmer2TextIndexer; yields query results’ key, offsets, 0.
-
__abstractmethods__
= frozenset({})¶
-