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

Module _base

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

Classes

_BaseExonerateParser
Abstract iterator for exonerate format.

_BaseExonerateIndexer
Indexer class for Exonerate plain text.

Functions

_set_frame(frag)
Sets the HSPFragment frames.

source code

_make_triplets(seq)
Splits a string into a list containing triplets of the original string.

source code

_adjust_aa_seq(fraglist)
Transforms three-letter amino acid codes into one-letters in the given HSPFragments.

source code

_split_fragment(frag)
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_hit_or_query_line(line)
Parse the 'Query:' line of exonerate alignment outputs.

source code

Variables

_STRAND_MAP = {'+': 1, '-': -1, '.': 0}

_RE_SHIFTS = re.compile(r'(#+)')

_RE_TRANS = re.compile(r'[53ISCF]')