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Thanks. However, BPlite is not in Bioperl 0.6.2 release, is it? I can't find
it under Tools. I do find Ian Korf's BPlite module, is this the one you were
talking about?
David
> -----Original Message-----
> From: Jason Stajich [SMTP:jason@chg.mc.duke.edu]
> Sent: Wednesday, October 11, 2000 6:19 AM
> To: Hilmar Lapp
> Cc: Zhao, David [PRI]; Bioperl
> Subject: Re: [Bioperl-l] parsing only the summary part of a blast
> report
>
> see the perldoc for Bio::Tools::BPlite for all the complete api.
>
> This script will parse and print all of the hits in your report.
>
> #!/usr/local/bin/perl -w
>
> use Bio::Tools::BPlite;
>
> my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
> print $report->query(), ",", $report->database(), "\n";
> while ( my $sbjct = $report->nextSbjct ) {
> print "name is ", $sbjct->name(), "\n";
> }
>
> Alternatively you can use Bio::Tools::Blast, but you will find it slower
> and more memory intensive. It does support more features so it depends on
> what your needs are.
>
> On Wed, 11 Oct 2000, Hilmar Lapp wrote:
>
> > > "Zhao, David [PRI]" wrote:
> > >
> > > Hi there,
> > > How can I parse the summary part of a blast report using bioperl
> > > modules? such as:
> > >
> >
> > I'm almost sure you can't using Blast.pm. Maybe you can with BPlite
> > (development trunk only). I know that Blast.pm takes a signifant time to
> > parse long reports (i.e., with hundreds of alignments), but we haven't
> > checked yet whether BPlite is significantly faster in such cases. I
> guess
> > you're asking because you bother about the time lost in parsing the
> > alignments, although you needed only the summary data which are already
> > present in the hit list.
> >
> > BTW you can pass a significance threshold to Blast.pm, and although I'm
> > not sure I think it won't parse those alignments beyond the significance
> > threshold.
>
> [Regarding Bio::Tools::Blast]
>
> I'm pretty sure the signifigance threshold only applies to when you are
> running Blast not parsing a report. In fact you should not put a
> signif=>$value in your parameter hash if you are just parsing a report
> file.
>
> >
> > Hilmar
> > --
> > -----------------------------------------------------------------
> > Hilmar Lapp email: hlapp@gmx.net
> > NFI Vienna, IFD/Bioinformatics phone: +43 1 86634 631
> > A-1235 Vienna fax: +43 1 86634 727
> > -----------------------------------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office)
> (919)684-2275 (fax)
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/
>
>
>
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<TITLE>RE: [Bioperl-l] parsing only the summary part of a blast =
report</TITLE>
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<BODY>
<P><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">Thanks. However, =
BPlite is not in Bioperl 0.6.2 release, is it? I can't find it under =
Tools. I do find Ian Korf's BPlite module, is this the one you were =
talking about?</FONT></P>
<P><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">David</FONT>
</P>
<BR>
<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 Stajich =
[SMTP:jason@chg.mc.duke.edu]</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">Sent: </FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Wednesday, October 11, 2000 6:19 AM</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">To: </FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">Hilmar Lapp</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Cc: </FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">Zhao, David [PRI]; Bioperl</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Subject: </FONT>=
</B> <FONT SIZE=3D1 FACE=3D"Arial">Re: [Bioperl-l] parsing only the =
summary part of a blast report</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">see the perldoc for Bio::Tools::BPlite =
for all the complete api.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">This script will parse and print all =
of the hits in your report.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">#!/usr/local/bin/perl -w</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">use Bio::Tools::BPlite;</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">my $report =3D new =
Bio::Tools::BPlite(-fh=3D>\*STDIN);</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">print $report->query(), =
",", $report->database(), "\n";</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">while ( my $sbjct =3D =
$report->nextSbjct ) {</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"> print "name =
is ", $sbjct->name(), "\n";</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">}</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Alternatively you can use =
Bio::Tools::Blast, but you will find it slower</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">and more memory intensive. It =
does support more features so it depends on</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">what your needs are.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">On Wed, 11 Oct 2000, Hilmar Lapp =
wrote:</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">> > "Zhao, David =
[PRI]" wrote:</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> > </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> > Hi there,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> > How can I parse the summary =
part of a blast report using bioperl</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> > modules? such as:</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> > </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> I'm almost sure you can't using =
Blast.pm. Maybe you can with BPlite</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> (development trunk only). I know =
that Blast.pm takes a signifant time to</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> parse long reports (i.e., =
with hundreds of alignments), but we haven't</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> checked yet whether BPlite is =
significantly faster in such cases. I guess</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> you're asking because you bother =
about the time lost in parsing the</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> alignments, although you needed =
only the summary data which are already</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> present in the hit list.</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> BTW you can pass a significance =
threshold to Blast.pm, and although I'm</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> not sure I think it won't parse =
those alignments beyond the significance</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> threshold.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">[Regarding Bio::Tools::Blast]</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">I'm pretty sure the signifigance =
threshold only applies to when you are</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">running Blast not parsing a =
report. In fact you should not put a</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">signif=3D>$value in your parameter =
hash if you are just parsing a report</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">file.</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">> </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> =
Hilmar</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> -- </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> =
-----------------------------------------------------------------</FONT>=
<BR><FONT SIZE=3D2 FACE=3D"Arial">> Hilmar =
Lapp &n=
bsp; &n=
bsp; email: =
hlapp@gmx.net</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> NFI Vienna, =
IFD/Bioinformatics =
phone: +43 1 86634 631</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> A-1235 =
Vienna =
=
fax: +43 1 86634 =
727</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> =
-----------------------------------------------------------------</FONT>=
<BR><FONT SIZE=3D2 FACE=3D"Arial">> =
_______________________________________________</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> Bioperl-l mailing list</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> Bioperl-l@bioperl.org</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> <A =
HREF=3D"http://bioperl.org/mailman/listinfo/bioperl-l" =
TARGET=3D"_blank">http://bioperl.org/mailman/listinfo/bioperl-l</A></FON=
T>
<BR><FONT SIZE=3D2 FACE=3D"Arial">> </FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Arial">Jason Stajich</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">jason@chg.mc.duke.edu</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://galton.mc.duke.edu/~jason/" =
TARGET=3D"_blank">http://galton.mc.duke.edu/~jason/</A></FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">(919)684-1806 (office) </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">(919)684-2275 (fax) </FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Center for Human Genetics - Duke =
University Medical Center</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://wwwchg.mc.duke.edu/" =
TARGET=3D"_blank">http://wwwchg.mc.duke.edu/</A> </FONT>
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