[Bioperl-l] SearchIO question

[Brian Osborne]

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

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