Package Bio :: Package SearchIO :: Package HmmerIO :: Module hmmer3_text
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Module hmmer3_text

source code

Bio.SearchIO parser for HMMER plain text output format.
Classes [hide private]
  Hmmer3TextParser
Parser for the HMMER 3.0 text output.
  Hmmer3TextIndexer
Indexer class for HMMER plain text output.
Variables [hide private]
  _RE_PROGRAM = re.compile(r'^# (\w*hmm\w+) :: .*$')
  _RE_VERSION = re.compile(r'# \w+ ([\w\+\.]+) .*; http.*$')
  _RE_OPT = re.compile(r'^# (.+):\s+(.+)$')
  _QRE_ID_LEN_PTN = '^Query:\\s*(.*)\\s+\\[\\w=(\\d+)\\]'
  _QRE_ID_LEN = re.compile(r'^Query:\s*(.*)\s+\[\w=(\d+)\]')
  _HRE_VALIDATE = re.compile(r'score:\s(-?\d+\.?\d+)\sbits.*valu...
  _HRE_ANNOT_LINE = re.compile(r'^(\s+)(.+)\s(\w+)')
  _HRE_ID_LINE = re.compile(r'^(\s+\S+\s+[0-9-]+ )(.+?)(\s+[0-9-...
  __package__ = 'Bio.SearchIO.HmmerIO'
Variables Details [hide private]

_HRE_VALIDATE

Value:
re.compile(r'score:\s(-?\d+\.?\d+)\sbits.*value:\s(.*)')

_HRE_ID_LINE

Value:
re.compile(r'^(\s+\S+\s+[0-9-]+ )(.+?)(\s+[0-9-]+)')