On Mon, Aug 15, 2011 at 11:43 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi Jeremy,
>
> Things do indeed look much better after your commit last night, thanks:
> https://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157
>
> On Mon, Aug 15, 2011 at 12:52 AM, Jeremy Goecks <jeremy.goe...@emory.edu> 
> wrote:
>>> Well, sort of. After converting that GFF3 file into BED, the strand column
>>> isn't set in the metadata. That seems important!
>>
>> We'll look into this.
>
> Thanks. If I manually set the BED strand to column 5, then the extract tool
> can be used with both the original NCBI GFF3 file and the BED conversion.
> I have filtered these on gene features, and noticed a discrepancy.
>
> GFF uses one based numbering, e.g. the gene NEQ003 is 883 to 2691.
>
> For BED the start coordinate is zero-indexed and the end coordinate is
> one-indexed (just like Python slicing), thus the gene NEQ003 is 882 to
> 2691 (and Galaxy converts this correctly).
>
> Using the extract tool with the gene features correctly get the nucleotide
> sequence of NEQ003 running from ATG...TAA regardless of if I use the
> genes in GFF3 format or in BED format (good).
>
> However, the FASTA output uses different names because it embeds
> the start/end co-ordindates as is. Thus using GFF3 features, the
> sequence name includes _883_2691_ while using BED features the
> same sequence has instead _882_2691_ for its name.
>
> I propose this be harmonised by always using one-based counting
> in the FASTA names (as done in GFF files but also GenBank, EMBL,
> etc) rather than the convention used in BED files (and Python) which
> is confusing to most non-programmers.

i.e. I suggest this change (with new tests to enforce it),

https://bitbucket.org/peterjc/galaxy-central/changeset/e7393df0fbc1

This is currently the one and only commit on this new branch,

https://bitbucket.org/peterjc/galaxy-central/src/extract_region2

Peter
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