[Bioperl-l] more question about extracting information from G FF file

[Marc Logghe]

This should do it:

#!/usr/bin/perl -w
use strict;
use Bio::Tools::GFF;

my $gff = Bio::Tools::GFF->new(-fh => \*STDIN);

while (my $f = $gff->next_feature)
{
  print $f->get_tag_values('Sequence'),"\n" ;

}
Marc

> -----Original Message-----
> From: Jack Chen [mailto:chenn at cshl.edu]
> Sent: Thursday, April 10, 2003 2:31 AM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] more question about extracting 
> information from GFF
> file
> 
> 
> To: bioperl-l at bioperl.org
> Subject: more questions about parsing gff files
> Parts/Attachments:
>    1 Shown     21 lines  Text
>    2   OK    ~736 bytes  Text, ""
> ----------------------------------------
> 
> Hi All,
> 
> I'd like to ask you for assistance on how to extract some 
> fields from gff
> files. Say from the attached file, I'd like to get the 
> sequence name (the 
> string inside the double quotes). Could you please show me how to do
> this? I have tried methods from the Bio::SeqFeatureI module 
> but none of
> them do the trick.
> 
> Thanks,
> 
> Jack
> 
> Example file:
> 
> CHROMOSOME_I    curated exon    5959876 5959878 .       -       0
> Sequence "B0207.8"   
> CHROMOSOME_I    curated exon    10079837        10079839      
>   .       -
> 0       Sequence "B0379.2"   
> CHROMOSOME_I    curated exon    6628806 6628808 .       +       0
> Sequence "D2092.8"   
> CHROMOSOME_I    curated exon    9171713 9171715 .       +       0
> Sequence "F25H5.4"   
> CHROMOSOME_I    curated exon    7356125 7356126 .       +       2
> Sequence "F52A8.6b"   
> CHROMOSOME_I    curated exon    5020062 5020064 .       -       0
> Sequence "F54C1.7"   
> CHROMOSOME_I    curated exon    6149532 6149534 .       +       0
> Sequence "F56F4.3"   
> CHROMOSOME_I    curated exon    13333412        13333414      
>   .       +
> 0       Sequence "T04D3.4"   
> CHROMOSOME_I    curated exon    6162206 6162208 .       +       0
> Sequence "T09B4.5"   
> HROMOSOME_X     curated exon    9493440 9493442 .       -       0
> Sequence "ZK899.4"   
> 
> 
> +-----O----------------------------------------+
> |    o-o     Jack Chen, Stein Laboratory       |
> |    o---o   Cold Spring Harbor Laboratory     |
> |  o----o    1 Bungtown Road                   |
> | O----O     Cold Spring Harbor, NY, 11724     |
> | 0--o       Tel: 1 516 367 8394               |
> |   O        Website: http://www.wormbase.org  |
> |  o-o       e-mail: chenn at cshl.org            |
> +-o---o----------------------------------------+ 
> 
> 
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