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view rDiff/src/tools/compute_testing_region.m @ 2:233c30f91d66

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updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
parents 0f80a5141704
children
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function [genes]=compute_testing_region(CFG,genes)

%Iterate over gene

for i=1:size(genes,2)
    [SPLICINGEVENTS,SEQUENCE,EXONSEQUENCE]=splicingsequence(genes(i));
    genes(i).splicingevents=SPLICINGEVENTS;
    genes(i).sequence=SEQUENCE;
    genes(i).exonsequence=EXONSEQUENCE;
    
    [UNIQUE_NEW_EXONS,GRAPHNODES,ORDER_OF_GRAPHNODE,EIRS_IN_SEQ]=transform_single_end_reads(genes(i),CFG.sequenced_length-CFG.bases_to_clip*2);
    genes(i).unique_new_exons=UNIQUE_NEW_EXONS;
    genes(i).graphnodes=GRAPHNODES;
    genes(i).order_of_graphnodes=ORDER_OF_GRAPHNODE;
    genes(i).eirs_in_seq=EIRS_IN_SEQ;
 
end