Hi Adhemar,

Very glad this is working out for your own use. I created a ticket to include your suggested enhancement globally:
https://trello.com/c/jbhy3dSM

Should you wish to create a ticket in the future, this is how:
https://wiki.galaxyproject.org/Issues

Community contributions are reviewed/incorporated through pull-requests, if you would like to submit. No guarantees, but either way this moves it along and you'll then know the status:
https://wiki.galaxyproject.org/Develop
-> See ' Source code and documentation'
https://bitbucket.org/galaxy/galaxy-central/pull-requests

Best,

Jen
Galaxy team

On 3/28/14 5:41 AM, Adhemar wrote:

Hi,
In order to have the transcript_id for each sequence extracted from the cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding the following lines after line 153:

attributes = gff_util.parse_gff_attributes( feature[8] )

if ( "transcript_id" in attributes ):

name = attributes.get( "transcript_id", None )

This way the variable name gets the transcript_id if it exists.

If it's correct, I would appreciate this modification in future galaxy distributions.

Thanks!

Adhemar
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