<div dir="ltr">David, could you please mail me said scripts? I'm gonna make a reader library, perhaps SeqIO-compatible and it'll be great if I can reuse your code. I think mailing list doesn't support file attachments, so please use my e-mail or some file hosting.<div>Blastdbcmd is a nice thing, and may indeed need a wrapper, but I can easily imagine a situation when one has a DB, but doesn't have blastdbcmd (I'm in such a situation myself, actually, and installing software to the cluster we use may be a hassle). So I'd rather have a code with as little dependencies as possible.<br><div><div class="gmail_extra"><br><div class="gmail_quote">2015-03-04 18:22 GMT+08:00 Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi David,<br>
<br>
If you run a BLAST search you can get the ID of a matched sequence<br>
(and the matching region of the sequence). Using blastdbcmd you<br>
can get the entire matching sequence from the BLAST DB using<br>
their ID (or ask for multiple sequences by giving several IDs). The<br>
sequences can be output in FASTA format.<br>
<br>
Note Bio.Blast.Applications doesn't yet have a wrapper to help<br>
calling blastdbcmd from within Python - that would be a nice addition.<br>
<span><font color="#888888"><br>
Peter<br>
</font></span><div><div><br>
On Wed, Mar 4, 2015 at 9:59 AM, David Shin <<a href="mailto:davidsshin@lbl.gov" target="_blank">davidsshin@lbl.gov</a>> wrote:<br>
> Hi Peter,<br>
><br>
> If I understand Alexey's question right, I did have the same problem before.<br>
> I wrote a bunch of scripts to work around the problem, but it appears you<br>
> have something more straight forward. Can you elaborate?<br>
><br>
> Thanks,<br>
><br>
> Dave<br>
><br>
> On Wed, Mar 4, 2015 at 1:18 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
> wrote:<br>
>><br>
>> On Wed, Mar 4, 2015 at 6:12 AM, Alexey Morozov<br>
>> <<a href="mailto:alexeymorozov1991@gmail.com" target="_blank">alexeymorozov1991@gmail.com</a>> wrote:<br>
>> > Is there any support for compiled BLAST databases (*.pin/*.phr/*.psq)<br>
>> > I/O in<br>
>> > biopython? I need to get complete sequences that match, not just hsps<br>
>> > that<br>
>> > Bio.Blast.NCBIXML can read.<br>
>><br>
>> No, but you can call the NCBI BLAST+ tool blastdbcmd to do this<br>
>> (or fastacmd from legacy NCBI BLAST).<br>
>><br>
>> Peter<br>
>> _______________________________________________<br>
>> Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org" target="_blank">Biopython@mailman.open-bio.org</a><br>
>> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
><br>
><br>
><br>
><br>
> --<br>
> David Shin, Ph.D<br>
> Lawrence Berkeley National Labs<br>
> 1 Cyclotron Road<br>
> MS 83-R0101<br>
> Berkeley, CA 94720<br>
> USA<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div><font face="arial,helvetica,sans-serif">Alexey Morozov,<br>LIN SB RAS, bioinformatics group.<br>Irkutsk, Russia.<br></font></div>
</div></div></div></div>