Changeset 206

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Timestamp:
04/24/09 17:41:35 (7 months ago)
Author:
cholt
Message:

fix add_utr_gff

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  • README

    r199 r206  
    504504add_utr_gff.pl with the following command: 
    505505 
    506 maker2zff.pl <directory> 
     506add_utr_gff.pl <directory> 
    507507 
    508508    * <directory> is the directory where all of your GFF files are 
    …… 
    538538       maker2zff.pl <directory> genome 
    539539 
    540        * <directory> is the directory where all of your GFF3 files are 
     540       * <directory> a the directory where all of your GFF3 files are 
    541541         located 
    542542       * geneome is the name for the outfile 

  • bin/add_utr_gff.pl

    r205 r206  
    3838            if ($tag eq "mRNA") { 
    3939                my @id = $feature->get_tag_values('ID'); 
    40                 my $id = (split(/\s+/, $id[0]->as_text))[1]; 
     40                my $id = $id[0]; 
    4141                my @name = $feature->get_tag_values('Name'); 
    42                 my $name = (split(/\s+/, $name[0]->as_text))[1]; 
     42                my $name = $name[0]; 
    4343                $id2name{$id} = $name; 
    4444                $strand{$name} = $feature->strand; 
    …… 
    4646                my @parents = $feature->get_tag_values('Parent'); 
    4747                foreach my $p (@parents) { 
    48                     my $pid = (split(/\s+/, $p->as_text))[1]; 
     48                    my $pid = $p; 
    4949                    my $pname = $id2name{$pid}; 
    5050                    $strand{$pname} = $feature->strand; 
    …… 
    5454                my @parents = $feature->get_tag_values('Parent'); 
    5555                foreach my $p (@parents) { 
    56                     my $pid = (split(/\s+/, $p->as_text))[1]; 
     56                    my $pid = $p; 
    5757                    my $pname = $id2name{$pid}; 
    5858                    push @{$exons{$pname}}, ($start, $end);