[Bioperl-l] SearchIO question

[Brian Osborne]

Shin,

> I was using Steve's psiblast
>$result->no_hits_found() method.  Is this going to be phased out?

I can't speak for Steve, but he typically provides a multitude of novel and
useful methods to the user. Your thoughts, Steve?

Brian O.


-----Original Message-----
From: Shin Enomoto [mailto:shin at cbs.umn.edu]
Sent: Friday, March 07, 2003 11:44 AM
To: Brian Osborne
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] SearchIO question

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?

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?

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