diff variant_effect_predictor/Bio/AlignIO/bl2seq.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/bl2seq.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,190 @@
+# $Id: bl2seq.pm,v 1.13.2.1 2003/06/18 12:19:52 jason Exp $
+#
+# BioPerl module for Bio::AlignIO::bl2seq
+
+#	based on the Bio::SeqIO modules
+#       by Ewan Birney <[e-mail]>
+#       and Lincoln Stein  <[e-mail]>
+#
+#	the Bio::Tools::BPlite modules by
+#	Ian Korf ([e-mail], http://sapiens.wustl.edu/~ikorf),
+#	Lorenz Pollak ([e-mail], bioperl port)
+#
+#       and the SimpleAlign.pm module of Ewan Birney
+#
+# Copyright Peter Schattner
+#
+# You may distribute this module under the same terms as perl itself
+# _history
+# September 5, 2000
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
+
+=head1 SYNOPSIS
+
+Do not use this module directly.  Use it via the L<Bio::AlignIO> class, as in:
+
+    use Bio::AlignIO;
+
+    $in  = Bio::AlignIO->new(-file => "inputfilename" , '-format' => 'bl2seq');
+    $aln = $in->next_aln();
+
+
+=head1 DESCRIPTION
+
+This object can create L<Bio::SimpleAlign> sequence alignment objects (of
+2 sequences) from bl2seq BLAST reports.
+
+A nice feature of this module is that- in combination with
+StandAloneBlast.pm or remote blasting - it can be used to align 2
+sequences and make a SimpleAlign object from them which can then be
+manipulated using any SimpleAlign.pm methods, eg:
+
+   #Get 2 sequences
+   $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
+   my $seq3 = $str->next_seq();
+   my $seq4 = $str->next_seq();
+
+   # Run bl2seq on them
+   $factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp', 
+					       'outfile' => 'bl2seq.out');
+   my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
+
+   # Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
+   $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
+   $aln = $str->next_aln();
+
+   Pass in -report_type flag when initializing the object to have this
+   pass through to the Bio::Tools::BPbl2seq object.  See that object.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]               - General discussion
+  http://bio.perl.org/MailList.html   - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Peter Schattner
+
+Email: [e-mail]
+
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::AlignIO::bl2seq;
+use vars qw(@ISA);
+use strict;
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::AlignIO;
+use Bio::Tools::BPbl2seq;
+
+@ISA = qw(Bio::AlignIO);
+
+
+
+sub _initialize {
+    my ($self,@args) = @_;
+    $self->SUPER::_initialize(@args);
+    ($self->{'report_type'}) = $self->_rearrange([qw(REPORT_TYPE)],
+						 @args);
+    return 1;
+}
+
+=head2 next_aln
+
+ Title   : next_aln
+ Usage   : $aln = $stream->next_aln()
+ Function: returns the next alignment in the stream.
+ Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
+	    or on error
+ Args    : NONE
+
+=cut
+
+sub next_aln {
+    my $self = shift;
+    my ($start,$end,$name,$seqname,$seq,$seqchar);
+    my $aln =  Bio::SimpleAlign->new(-source => 'bl2seq');
+    $self->{'bl2seqobj'} =
+    	$self->{'bl2seqobj'} || Bio::Tools::BPbl2seq->new(-fh => $self->_fh,
+							  -report_type => $self->{'report_type'});
+    my $bl2seqobj = $self->{'bl2seqobj'};
+    my $hsp =   $bl2seqobj->next_feature;
+    $seqchar = $hsp->querySeq;
+    $start = $hsp->query->start;
+    $end = $hsp->query->end;
+    $seqname = 'Query-sequence';    # Query name not present in bl2seq report
+
+#    unless ($seqchar && $start && $end  && $seqname) {return 0} ;	
+    unless ($seqchar && $start && $end ) {return 0} ;	
+
+    $seq = new Bio::LocatableSeq('-seq'=>$seqchar,
+				 '-id'=>$seqname,
+				 '-start'=>$start,
+				 '-end'=>$end,
+				 );
+
+    $aln->add_seq($seq);
+
+    $seqchar = $hsp->sbjctSeq;
+    $start = $hsp->hit->start;
+    $end = $hsp->hit->end;
+    $seqname = $bl2seqobj->sbjctName;
+
+    unless ($seqchar && $start && $end  && $seqname) {return 0} ;	
+
+    $seq = new Bio::LocatableSeq('-seq'=>$seqchar,
+				 '-id'=>$seqname,
+				 '-start'=>$start,
+				 '-end'=>$end,
+				 );
+
+    $aln->add_seq($seq);
+
+    return $aln;
+
+}
+	
+
+=head2 write_aln
+
+ Title   : write_aln
+ Usage   : $stream->write_aln(@aln)
+ Function: writes the $aln object into the stream in bl2seq format
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+    my ($self,@aln) = @_;
+
+    $self->throw("Sorry: writing bl2seq output is not available! /n");
+}
+
+1;