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,