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

Module hmmer3_text

Bio.SearchIO parser for HMMER plain text output format.

Classes

Hmmer3TextParser
Parser for the HMMER 3.0 text output.

Hmmer3TextIndexer
Indexer class for HMMER plain text output.

Variables

_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-...

Variables Details

Value:

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

Value:

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