Bio::Tools::GFF, Target Tag disappears when editing a gff3 file

[cjfields]

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Author Name: Fred empty (Fred empty) Original Redmine Issue: 2953, https://redmine.open-bio.org/issues/2953 Original Date: 2009-11-25 Original Assignee: Bioperl Guts

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When using Bio::Tools::GFF for editing a GFF3 file, the edited file does not hold anymore Target tags !

($Id: GFF.pm 16330 2009-11-04 16:53:24Z)

[cjfields]

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Original Redmine Comment Author Name: Fred empty Original Date: 2009-11-25T08:25:52Z

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Created an attachment (id=1403) Blast sample file

Please find here a Blast sample file.

[cjfields]

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Original Redmine Comment Author Name: Fred empty Original Date: 2009-11-25T08:27:29Z

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I work with a sample Blast file (see attachment)

I make the original gff file : bp_search2gff.pl -v 3 -t query -i dcr1_sp.WUBLASTP -target -m -method match_part -o dcr1_sp.WUBLASTP.gff3

And then i try to add a new Tag : test.pl dcr1_sp.WUBLASTP.gff3

I use this sample code (test.pl) :

!/usr/local/bin/perl -w

use strict; use diagnostics; use warnings;

use Bio::Tools::GFF;

my $fileGFF3 = $ARGV[0];

my $in = new Bio::Tools::GFF( -gff_version => 3, -file => “$fileGFF3” ); my $out = new Bio::Tools::GFF( -gff_version => 3, -file => “>$fileGFF3.out” ); while ( my $seqfeature = $in->next_feature() ) {

if ( $seqfeature->primary_tag eq ‘match’ ) { $seqfeature->add_tag_value( ‘myNewTag’, “ValueOfMyNewTag” ); $out->write_feature($seqfeature);

} else { $out->write_feature($seqfeature); } } $out->close; exit;

[cjfields]

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Original Redmine Comment Author Name: Fred empty Original Date: 2009-11-25T08:35:05Z

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Bug 2952 has been marked as a duplicate of this bug.