[Bioperl-guts-l] bioperl commit

Heikki Lehvaslaiho heikki at pub.open-bio.org
Fri Jan 30 13:18:34 EST 2004


heikki
Fri Jan 30 13:18:34 EST 2004
Update of /home/repository/bioperl/bioperl-live/Bio/AlignIO
In directory pub.open-bio.org:/tmp/cvs-serv7181/Bio/AlignIO

Modified Files:
	fasta.pm phylip.pm 
Added Files:
	largemultifasta.pm 
Log Message:
started adding sequence alignments that store sequences in a file. coding by Albert Vilella

bioperl-live/Bio/AlignIO largemultifasta.pm,NONE,1.1 fasta.pm,1.14,1.15 phylip.pm,1.26,1.27
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/fasta.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/bioperl/bioperl-live/Bio/AlignIO/fasta.pm	2003/07/19 22:35:44	1.14
+++ /home/repository/bioperl/bioperl-live/Bio/AlignIO/fasta.pm	2004/01/30 18:18:34	1.15
@@ -107,6 +107,7 @@
 					     '-end'        =>$end,
 					     );
 		$aln->add_seq($seq);
+                $self->debug("Reading $seqname");
 	    }
 	    $desc = $tempdesc;	
 	    $name = $tempname;
@@ -158,6 +159,7 @@
 	
 	$aln->add_seq($seq);
     }
+    $self->debug("Reading $seqname");
     my $alnlen = $aln->length;
     foreach my $seq ( $aln->each_seq ) {
 	if( $seq->length < $alnlen ) {

===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/phylip.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/bioperl/bioperl-live/Bio/AlignIO/phylip.pm	2003/03/28 22:39:54	1.26
+++ /home/repository/bioperl/bioperl-live/Bio/AlignIO/phylip.pm	2004/01/30 18:18:34	1.27
@@ -300,6 +300,7 @@
 		    $self->_print (sprintf("%".($idlength+3)."s",$dispname));
 		    $tempcount = $count;
 		    $index = 0;
+                    $self->debug("residue count: $count\n") if ($count%100000 == 0);
 		    while( ($tempcount + $idlength < $length) && ($index < 5)  ) {
 			$self->_print (sprintf("%s ",substr($hash{$name},
 							    $tempcount,



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