>> >> It turns out there sort of is, extract/extract_genomic_dna.xml >> >> However, as written it isn't clear to me how to make this work >> with general tabular files, and how it would behave with proteins >> (which in principle can be process the same way). >> >> It also appears to insist on having both start and end present >> (I want to be able to have these default to the start/end of the >> referenced parent sequence). >> >> Peter >> > > 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. If you plan to support a general tabular format, the GOPS tools provide examples of how to work with BED, GFF, and interval datasets. *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. 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/