On Thu, Aug 4, 2011 at 4:17 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Aug 3, 2011 at 4:56 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hi all,
>> I'm about to start working on a general tool for extracting sequences
>> (from FASTA etc) based on a tabular file describing desired regions
>> (this could be a BED or GFF3 file), giving a new sequence file with
>> one entry for each region in the tabular file. Essentially I want as
>> input columns describing:
>> * FASTA sequence ID
>> * Start
>> * End
>> * Strand (optional)
>> * Region ID for this sequence in the output file (optional)
>> In the case of a GFF3 input, those would be columns 1, 4, 5, 7 (with
>> the ID being hidden inside column 9). But this isn't really driven by
>> GFF3 where you'd probably not want to treat each line separately
>> anyway (compound features).
>> I'm thinking of very general examples like extracting general search
>> matches (BLAST, HMMER, motifs, etc), but specifically things like
>> cleaving proteins to remove a predicted signal peptide. This could
>> even be used for trimming of sequencing reads (for small datasets,
>> e.g. capillary reads).
>> Is there anything like this in Galaxy already? If so I can't find it ;)
>> I've also skimmed the tool shed.
> 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)?

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