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