[Bioperl-l] bp_genbank2gff3.pl

Scott Cain scott at scottcain.net
Sat Sep 18 06:08:26 EDT 2010


Hi Dave,

That seems perfectly reasonable.  If you could point out a GenBank
entry for which that does not happen, I could try to figure out why
not.

Scott


On Sat, Sep 18, 2010 at 10:20 AM, David Breimann
<david.breimann at gmail.com> wrote:
> Since locus_tag is an essential tag in genbank, I suggest locus_tag will be
> always added to the GFF last column if it exists in the genbank, whether it
> is used as ID in the GFF or not.
>
> On Sat, Sep 18, 2010 at 11:17 AM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Dave,
>>
>> bp_genbank2gff3.pl suffers from the fact that it has to deal with
>> GenBank files :-)  It was designed initially to work on whole genome
>> refseqs, and contains several ad hoc rules for trying to make it "do
>> the right thing."  In practice, it is not unusual for a post
>> processing step (either by hand or a quicky perl script) to be
>> required to really get it right.  I don't recall the specifics (if I
>> ever knew :-) for when and how the locus tag is used, but I do know
>> that there is a list of things that it will try to use for the ID, and
>> while the locus is on the list, I don't know where it comes in the
>> list, so it's possible that other items might supersede it.
>>
>> Scott
>>
>>
>> On Sat, Sep 18, 2010 at 10:05 AM, David Breimann
>> <david.breimann at gmail.com> wrote:
>> > Hello,
>> >
>> > I'm not sure how bp_genbank2gff3.pl works. Sometimes it adds a
>> > `locus_tag`
>> > in the fields and sometime it doesn't, even though the genabank has a
>> > locus
>> > tag.
>> > Also, is the ID always equivalent to the locus tag?
>> >
>> > Thanks,
>> > Dave
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



More information about the Bioperl-l mailing list