Package Bio :: Package SearchIO :: Package ExonerateIO :: Module _base
[hide private]
[frames] | no frames]

Module _base

source code

Bio.SearchIO abstract base parser for Exonerate standard output format.

Classes [hide private]
Abstract iterator for exonerate format.
Indexer class for Exonerate plain text.
Functions [hide private]
Sets the HSPFragment frames.
source code
Splits a string into a list containing triplets of the original string.
source code
Transforms three-letter amino acid codes into one-letters in the given HSPFragments.
source code
Splits one HSPFragment containing frame-shifted alignment into two.
source code
_create_hsp(hid, qid, hspd)
Returns a list of HSP objects from the given parsed HSP values.
source code
Parse the 'Query:' line of exonerate alignment outputs.
source code
Variables [hide private]
  _STRAND_MAP = {'+': 1, '-': -1, '.': 0}
  _RE_SHIFTS = re.compile(r'(#+)')
  _RE_TRANS = re.compile(r'[53ISCF]')
  __package__ = 'Bio.SearchIO.ExonerateIO'