>> 
>> 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.





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