[Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations

Joanne Chen joannec at bii.a-star.edu.sg
Wed Nov 15 21:11:31 EST 2006


Hi, 
I am a new user to BioPerl and am encountering some problems while parsing
location statements.

I have read the link
http://www.bioperl.org/wiki/FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or_EMBL_files_to_get_the_sub-locations.3F
and tried to implement this.

However I am encountering some problems.

Given a testcase:

CDS     join(752472..752685,752752..753298,753335..754039)


CDS     complement(637431..639525)
   

CDS    741745..741781


This means that my file has join, complement and simple location statements.

Using Bio::Location::SplitLocationI object to get the coordinates, my output is:

CDS     752472..752685,752752..753298,753335..754039

CDS

CDS


The complement and simple location statements were not parsed properly. Am I
using the right BioPerl module to parse? Kindly assist on the appropriate steps
to retrieve all 3 different location types. Thanks!


Joanne



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