[Bioperl-l] Bio::Blast object question
Zhao, David [PRI Non J&J]
DZhao1@prius.jnj.com
Thu, 20 Sep 2001 21:25:40 -0400
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Hi Jason,
I'm using bioperl 0.7.1, and Bio::Tools:Blast module to parse blast report.
The sequence database that gave me such as were actually NCBI databases
(patnt, pataa).
The description using bioperl module looks like this:
Sequence 1 from patent US
instead of
Sequence 1 from patent US 6096507
The patent number somehow got cut off.
Thanks,
David
> -----Original Message-----
> From: Jason Eric Stajich [SMTP:jason@cgt.mc.duke.edu]
> Sent: Thursday, September 20, 2001 6:17 PM
> To: Zhao, David [PRI Non J&J]
> Cc: 'bioperl-l@bioperl.org'
> Subject: Re: [Bioperl-l] Bio::Blast object question
>
> David - I've struggled with this sometimes with reports as well when the
> query database is badly formatted - are you working with a NCBI blastdb or
> your own ? I would pull out the line from the db which this hit sequence
> is from
> (% grep "^>.*accession") -- where accession is the accession are you
> are having trouble with.
>
> If you can send that information to the list we can probably figure out a
> way to patch the parser. To help us better need to know what he Blast
> module name is (Bio::Tools::Blast or Bio::Tools::BPlite) and what version
> of bioperl you are using.
>
> -jason
>
> On Thu, 20 Sep 2001, Zhao, David [PRI Non J&J] wrote:
>
> > Hi all,
> > When I use $hit->desc() method parsing blast report, sometimes I only
> get
> > partial description of the sequence,
> > what should I do to get the full description?
> > Thanks,
> > David
> >
> >
>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>
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<TITLE>RE: [Bioperl-l] Bio::Blast object question</TITLE>
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<P><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">Hi Jason,</FONT>
<BR><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">I'm using bioperl =
0.7.1, and Bio::Tools:Blast module to parse blast report. The sequence =
database that gave me such as were actually NCBI databases (patnt, =
pataa).</FONT></P>
<P><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">The description =
using bioperl module looks like this:</FONT>
</P>
<P><FONT FACE=3D"Times New Roman">Sequence 1 from patent US</FONT>
<BR><FONT FACE=3D"Times New Roman">instead of </FONT>
<BR><FONT FACE=3D"Times New Roman">Sequence 1 from patent US =
6096507</FONT>
<BR><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">The patent number =
somehow got cut off.</FONT>
<BR><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">Thanks,</FONT>
<BR><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial">David</FONT>
</P>
<BR>
<UL>
<P><FONT SIZE=3D1 FACE=3D"Arial">-----Original Message-----</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">From: </FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Jason Eric Stajich =
[SMTP:jason@cgt.mc.duke.edu]</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">Sent: </FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Thursday, September 20, 2001 6:17 PM</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">To: </FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">Zhao, David [PRI Non J&J]</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Cc: </FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">'bioperl-l@bioperl.org'</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Subject: </FONT>=
</B> <FONT SIZE=3D1 FACE=3D"Arial">Re: [Bioperl-l] Bio::Blast object =
question</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">David - I've struggled with this =
sometimes with reports as well when the</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">query database is badly formatted - =
are you working with a NCBI blastdb or</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">your own ? I would pull out the =
line from the db which this hit sequence</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">is from</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">(% grep "^>.*accession") =
-- where accession is the accession are you</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">are having trouble with.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">If you can send that information to =
the list we can probably figure out a</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">way to patch the parser. To =
help us better need to know what he Blast</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">module name is (Bio::Tools::Blast or =
Bio::Tools::BPlite) and what version</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">of bioperl you are using.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">-jason</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">On Thu, 20 Sep 2001, Zhao, David =
[PRI Non J&J] wrote:</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">> Hi all,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> When I use $hit->desc() =
method parsing blast report, sometimes I only get</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> partial description of the =
sequence,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> what should I do to get the full =
description?</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> Thanks,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> David</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">></FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">></FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">-- </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Jason Stajich</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Duke University</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">jason@cgt.mc.duke.edu</FONT>
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