I attempted to parse an old GenBank file (see URL below) to extract various features (which I would then want to write in GFF format). I encountered an error (please see below) when parsing the GenBank file with Biopython (version 1.64) using SeqIO.parse method to access the records.
Biopython error: /opt/apps/python/2.7.3/lib/python2.7/site-packages/Bio/GenBank/__init__.py:1108: BiopythonParserWarning: Couldn't parse feature location: 'AL3587126.96.36.199931:3274..3461'
I looked at the Bio/GenBank/__init__.py file and found many regular expressions that check the format of the feature locations and these regexps seem to include the format of the location I encounter i.e. 'AL3587188.8.131.52931:3274..3461' (please see the example regexp below for complex location from the __init__.py file). So I am not quite sure why the code raises the BiopythonParserWarning error.
Regexp in Bio/GenBank/__init__.py: _complex_location = r"([a-zA-z][a-zA-Z0-9_]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)" % (_pair_location, _solo_location, _between_location, _within_location, _oneof_location)
Could anybody please help me solve this parsing issue?
Thank you very much for your help.