Package obitools :: Package seqdb :: Package genbank :: Module parser
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Module parser

source code

Functions [hide private]
 
__gbparser(text) source code
 
genbankParser(text) source code
 
genbankIterator(file) source code
 
genpepParser(text) source code
 
genpepIterator(file) source code
Variables [hide private]
  _featureMatcher = re.compile(r'(?ms)^FEATURES.+\n(?=ORIGIN)')
  _headerMatcher = re.compile(r'(?ms)^LOCUS.+(?=\nFEATURES)')
  _seqMatcher = re.compile(r'(?ms)(?<=ORIGIN).+(?=//\n)')
  _cleanSeq = re.compile(r'[ \n0-9]+')
  _acMatcher = re.compile(r'(?m)(?<=^ACCESSION ).+')
  _deMatcher = re.compile(r'(?m)(?<=^DEFINITION ).+\n( .+\n)*')
  _cleanDe = re.compile(r'\n *')
  __package__ = 'obitools.seqdb.genbank'

Imports: re, sys, gb, nucEntryIterator, aaEntryIterator