Jeremy wrote:
Peter wrote:
Any thoughts from the Galaxy team? Are you open to making extract/extract_genomic_dna.xml more general - for instance renaming and rewording to indicate work on protein FASTA files as well as nucleotide FASTA files and reference genomes (assuming it does work)?
Peter,
We're open to enhancing this tool. Here are my thoughts:
*Enabling the tool to work with general tabular formats would seem to be a relatively low priority because it's easy to convert a general tabular file into a simple BED file by cutting columns.
For some of the example use cases I have in mind, I'd first have to generate a start column of ones (beginning of the sequence), and an end column of the length of the sequence. But yes, I can see how this could be done.
If you plan to support a general tabular format, the GOPS tools provide examples of how to work with BED, GFF, and interval datasets.
Putting GOPS into the Galaxy tool search brings up the Operate on Genomic Intervals section, is GOPS short genomic interval operations?
*The tool should work with general fasta files right now, so the changes needed to support protein and other fastas should be UI-based only.
Right, while of course preserving the (now misleading) tool ID of "Extract genomic DNA 1" and filename of extract/extract_genomic_dna.xml for backwards compatibility. I'll take a look at this then - thanks, Peter