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
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