Re: [galaxy-dev] extract_genomic_dna.py
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] extract_genomic_dna.py
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] extract_genomic_dna.py checks alignseq.loc?
Hi Holger, I went to the respective file and found that the line which defines seq_file is commented out: (l.38 in def check_seq_file()) ## seq_file = %s/alignseq.loc % GALAXY_DATA_INDEX_DIR This seems to be a bug in the current version of the file. There is clearly something amiss. In the galaxy-dist source, this line is not commented: https://bitbucket.org/galaxy/galaxy-dist/src/b258de1e6cea/tools/extract/extract_genomic_dna.py Removing the comment, the script tries to check for sequence entries in alignseq.loc, which I left empty before, since I didn't need aligned sequences in galaxy until now. Of course this results in another error: 'No sequences are available for 'hg19', request them by reporting this error.' This is the correct behavior. I just wanted to raise the question if this dependency is right, wouldn't one rather like to check for the respective build in faseq.loc (unfortunately the file format is different, it doesn't contain the seq in the first column). Yes, faseq.loc should be used. The use of alignseq.loc is a historical artifact that we haven't fixed yet. If you're inclined to fix it, we'd be happy to incorporate the changes into the code base. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
