Package Bio :: Package SearchIO :: Package ExonerateIO :: Module _base
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Module _base

source code

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

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