[Bioperl-l] SearchIO question

[Jason Stajich]

On Fri, 7 Mar 2003, Shin Enomoto wrote:

> Brian,
>
> I want to parse out the No hits. I was using Steve's psiblast
> $result->no_hits_found() method.  Is this going to be phased out? Is
> calling blast:: $result->num_hits and looking to see if it is 0 the way
> to go?
>
Sounds like a good way to go.

> I ran 6000 HMMER searches from Pfams against my genome using a shell
> script and dumped it out as a large report. Back in November, I tried
> using hmmer module to parse out this report. This only worked for the
> first result. Is there a plan to bring this under the genric module?
>
Did you try the SearchIO hmmer parser?

> On Friday, March 7, 2003, at 08:43  AM, Brian Osborne wrote:
>
> > Shin,
> >
> > The developers have been putting a lot of time on SearchIO recently. I
> > suggest you wait for v. 1.2.1, install it, and get back to Bioperl
> > with the
> > errors. The differences you're seeing are presumably due to different
> > versions, not different machines.
> >
> > With v. 1.2 all the methods you're calling with -format=>'blast' work
> > for
> > me. The script I used to demonstrate all of these methods is in the
> > package,
> > it's called examples/searchio/blast_example.pl.
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at bioperl.org
> > [mailto:bioperl-l-bounces at bioperl.org]On
> > Behalf Of Shin Enomoto
> > Sent: Friday, March 07, 2003 2:14 AM
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] SearchIO question
> >
> > I have been using SearchIO to parse NCBI BLAST reports on five
> > different computers with slightly different versions of BioPerl
> > installed. I also go back and forth between using Blast.pm and
> > PsiBlast.pm. I noticed erratic behavior in some of the parsing results
> > from very similar scripts.
> >
> > On one machine:
> > $hsp->end('hit') with blast  returns hit
> > $hsp->hit->end with psiblast returns a large number with a actual
> > number embedded within.
> >
> > $hsp->hit->end with blast returns the correct number.
> >
> > On this same machine:
> > $result->query_description with blast returns blank
> > $result->query_name with blast returns name and description as one
> > string
> > both of these work with psiblast normally.
> > The problem with using psiblast is that I cannot get $hsp->strand to
> > give me anything but 0s.
> >
> > Is there a simple explanation for these erratic behavior? Is there a
> > large table of all the methods encoded in the different modules from
> > different versions?
> >
> >
> >
> >
> >
> >
> >
> > Shin Enomoto
> > 295 ASLVM
> > 1988 Fitch Ave
> > St. Paul, MN 55108
> >
> > 612-625-7737
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> >
> >
> Shin Enomoto
> 295 ASLVM
> 1988 Fitch Ave
> St. Paul, MN 55108
>
> 612-625-7737
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu