Package Bio :: Package SearchIO :: Package ExonerateIO :: Module exonerate_vulgar

Module exonerate_vulgar

Bio.SearchIO parser for Exonerate vulgar output format.

Classes

ExonerateVulgarParser
Parser for Exonerate vulgar strings.

ExonerateVulgarIndexer
Indexer class for exonerate vulgar lines.

Functions

parse_vulgar_comp(hsp, vulgar_comp)
Parses the vulgar components present in the hsp dictionary.

source code

Variables

_RE_VULGAR = re.compile(r'(?x)^vulgar:\s+(\S+)\s+(\d+)\s+(\d+)...

_RE_VCOMP = re.compile(r'(?x)\s+(\S+)\s+(\d+)\s+(\d+)')

Variables Details

Value:

re.compile(r'(?x)^vulgar:\s+(\S+)\s+(\d+)\s+(\d+)\s+([\+-\.])\s+(\S+)\
s+(\d+)\s+(\d+)\s+([\+-\.])\s+(\d+)(\s+.*)$')