[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1119 (fwd)

[Jason Stajich]

It appears the psi module was missing, I'm not sure when that
functionality was worked on, but I went ahead and wrote a quick AlignIO
module that reads/writes the PSI-BLAST alignment format.
I tested it with the example data in the README.bls blast document so I
believe it works correctly now.
Added to branch and main trunk.


-jason


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

---------- Forwarded message ----------
Date: Tue, 12 Mar 2002 12:29:39 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1119

JitterBug notification

new message incoming/1119

Message summary for PR#1119
	From: spitzem@uni-muenster.de
	Subject: AlignIO/psi.pm missing
	Date: Tue, 12 Mar 2002 12:29:38 -0500
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From spitzem@uni-muenster.de Tue Mar 12 12:29:38 2002
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Date: Tue, 12 Mar 2002 12:29:38 -0500
Message-Id: <200203121729.g2CHTckO003102@pw600a.bioperl.org>
From: spitzem@uni-muenster.de
To: bioperl-bugs@bioperl.org
Subject: AlignIO/psi.pm missing

Full_Name: Michael Spitzer
Module: AlignIO
Version: 1.0alpha
PerlVer: 5.6.1
OS: Solaris 8
Submission from: emb057.uni-muenster.de (128.176.26.173)


Hi!

This is the same error/bug as described at the end of bug-report ID-959.
The following script produces the exception described at the bottom, it's
more or less an exact copy from the examples in the
StandAloneBlast-Documentation:

--- script ---
require v5.6.1;
use diagnostics;
use strict;
use Data::Dumper;
use lib "$ENV{HOME}/bin/perl/lib";
use Bio::Tools::Run::StandAloneBlast;
use Bio::AlignIO;

my $fasta = Bio::AlignIO->new('-file' => $param->{"in"}, '-format' => 'FASTA');
my $aln  = $fasta->next_aln;
my $len  = &aln_length;
my $mask = "1" x $len;
my $blastreport = $factory->blastpgp("ABCG1.fasta", $aln, $mask);
# crash-position
--- script ---

--- error message ---
Bio/AlignIO/psi.pm: psi cannot be found
Exception Uncaught exception from user code:
        Can't locate Bio/AlignIO/psi.pm in @INC (@INC contains:
/home/spitzem/working_dir/programming/perl
/home/spitzem/bin/perl/lib/5.6.1/sun4-solaris-multi
/home/spitzem/bin/perl/lib/5.6.1 /home/spitzem/bin/perl/lib
/v/gnu/perl/lib/5.6.1/sun4-solaris-multi /v/gnu/perl/lib/5.6.1
/v/gnu/perl/lib/site_perl/5.6.1/sun4-solaris-multi
/v/gnu/perl/lib/site_perl/5.6.1 /v/gnu/perl/lib/site_perl .) at
/home/spitzem/bin/perl/lib/Bio/AlignIO.pm line 380, <GEN0> line 10.
        eval {...} called at /home/spitzem/bin/perl/lib/Bio/AlignIO.pm line 379
        Bio::AlignIO::_load_format_module('psi') called at
/home/spitzem/bin/perl/lib/Bio/AlignIO.pm line 304
        Bio::AlignIO::new('Bio::AlignIO', '-fh', 'GLOB(0x636394)', '-format',
'psi') called at /home/spitzem/bin/perl/lib/Bio/Tools/Run/StandAloneBlast.pm
line 726
        Bio::Tools::Run::StandAloneBlast::_setinput('Bio::Tools::Run::StandAloneBlast=HASH(0x32d94)',
'blastpgp', 'ABCG1.fasta', 'Bio::SimpleAlign=HASH(0x631ad4)',
1111111111111111111111111111111111111111111111111111111111111111...) called at
/home/spitzem/bin/perl/lib/Bio/Tools/Run/StandAloneBlast.pm line 497
        Bio::Tools::Run::StandAloneBlast::blastpgp('Bio::Tools::Run::StandAloneBlast=HASH(0x32d94)',
'ABCG1.fasta', 'Bio::SimpleAlign=HASH(0x631ad4)',
1111111111111111111111111111111111111111111111111111111111111111...) called at
/home/spitzem/working_dir/programming/perl/retr_localblast.pl line 118

For more information about the AlignIO system please see the AlignIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "write_aln" on an undefined value at
        /home/spitzem/bin/perl/lib/Bio/Tools/Run/StandAloneBlast.pm line 727,
<GEN0> line 10 (#1)
    (F) You used the syntax of a method call, but the slot filled by the
    object reference or package name contains an undefined value.  Something
    like this will reproduce the error:

        $BADREF = undef;
        process $BADREF 1,2,3;
        $BADREF->process(1,2,3);

Uncaught exception from user code:
        Can't call method "write_aln" on an undefined value at
/home/spitzem/bin/perl/lib/Bio/Tools/Run/StandAloneBlast.pm line 727, <GEN0>
line 10.
        Bio::Tools::Run::StandAloneBlast::_setinput('Bio::Tools::Run::StandAloneBlast=HASH(0x32d94)',
'blastpgp', 'ABCG1.fasta', 'Bio::SimpleAlign=HASH(0x631ad4)',
1111111111111111111111111111111111111111111111111111111111111111...) called at
/home/spitzem/bin/perl/lib/Bio/Tools/Run/StandAloneBlast.pm line 497
        Bio::Tools::Run::StandAloneBlast::blastpgp('Bio::Tools::Run::StandAloneBlast=HASH(0x32d94)',
'ABCG1.fasta', 'Bio::SimpleAlign=HASH(0x631ad4)',
1111111111111111111111111111111111111111111111111111111111111111...) called at
/home/spitzem/working_dir/programming/perl/retr_localblast.pl line 118
--- error message ---

The 'psi.pm' seems not to be included anywhere in the
bioperl-1.0alpha-distribution.

Thanks in advance!

Micha


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