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# $Id: Analysis.pm,v 1.2 2004/11/24 02:28:00 cmungall Exp $
#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::IO::Analysis;
=head1 NAME
GO::IO::Analysis - preliminary analysis object
=head1 SYNOPSIS
=cut
=head1 DESCRIPTION
top level module for doing analyses eg clustalw on the fly
=head1 CREDITS
=head1 PUBLIC METHODS
=cut
use strict;
use base qw(GO::Model::Root);
use GO::Utils qw(rearrange);
#use GO::IO::Blast;
sub _valid_params { qw() };
sub clustalw {
my $self = shift;
my ($products, $seqs, $seqf) = rearrange([qw(products seqs file)], @_);
my $leave = $seqf ? 1 : 0;
if (!$seqs) {
$seqs = [];
my %h = ();
foreach my $p (@$products) {
push(@$seqs,
grep {
!$h{$_->display_id} && ($h{$_->display_id} = 1)
} @{$p->seq_list});
}
}
# TODO : use displatcher class to allow
# other ways of calling programs
my $seqf = $seqf || "/tmp/$$.clustalin.fa";
my $outf = $seqf;
$outf =~ s/fa$/aln/;
open(F, ">$seqf") || die;
map {print F $_->to_fasta} @$seqs;
close(F);
my $cmd = "clustalw -infile=$seqf -outfile=$outf";
print "cmd=$cmd\n";
print `$cmd`;
open(F, "$outf") || die;
my $out = join("", <F>);
close(F);
unless ($leave) {
unlink $seqf;
unlink $outf;
}
return $out;
}
#sub blastp {
# my $self = shift;
# my ($fn) = rearrange([qw(file)], @_);
# # TODO : use displatcher class to allow
# # other ways of calling programs
# #HARDCODE ALERT!!!!!!!!!!!!!!!!!!!!
# # this is a still a VERY preliminary module
# my $db = "/www/whitefly_80/WWW/annot/go/fasta/go_pep.fa";
# my $outf = "/tmp/$$.blastout.fa";
## my $cmd = "blastp $db $fn -filter SEG+XNU > $outf";
# my $cmd = "blastp $db $fn > $outf";
# print "cmd=$cmd\n";
# print `$cmd`;
# my $blast =
# GO::IO::Blast->new({apph=>$self->apph,
# file=>"$outf"});
# return $blast;
#}
=head1 FEEDBACK
Email cjm@fruitfly.berkeley.edu
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself
=cut
1;
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