[Bioperl-guts-l] bioperl-live/Bio/Tools RNAMotif.pm,1.10,1.10.4.1

[Senduran Balasubramaniam]

Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory dev.open-bio.org:/tmp/cvs-serv10682/Bio/Tools

Modified Files:
      Tag: branch-1-5-2
	RNAMotif.pm 
Log Message:
merge from HEAD, bugfixes and new PullParserI and hmmer parser

Index: RNAMotif.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RNAMotif.pm,v
retrieving revision 1.10
retrieving revision 1.10.4.1
diff -C2 -d -r1.10 -r1.10.4.1
*** RNAMotif.pm	7 Aug 2006 17:24:09 -0000	1.10
--- RNAMotif.pm	20 Aug 2006 22:03:30 -0000	1.10.4.1
***************
*** 316,336 ****
              if(/^#RM\sdescr\s(.*)$/) { # contains sec structure
                  $self->{'_sec_structure'}=$1;
-                 $self->debug("Found descriptor: $self->{'_sec_structure'}\n");
              }
              if(/^#RM\sdfile\s(.*)$/) { # contains dfile
                  $self->{'_dfile'}=$1;
-                 $self->debug("Found dfile : $self->{'_dfile'}\n");
              }
              $_ = $self->_readline;
          }
          if(m/^>((\S*)\s.*)$/) {
-             $self->debug("Found a description: $1\n");
              $seqid = $2;
              $description = $1; # contains entire description line if needed
-             # try to get accession from FASTA-like header (if from Genbank) otherwise punt
-             # Thanks to J. Stajich for this idea, which is part of SeqIO now
              if($seqid =~  /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|/) {
                  $seqid = $2; # pulls out gid
-                 $self->debug("Genbank gid: $seqid\n");
              }
          }
--- 316,330 ----
***************
*** 353,360 ****
                  ($start, $end, $strand) = ($end, $start, -1);
              }
-             if($score =~ /[a-zA-Z\s]/) { #probably containing extra data from sprintf()
-                 $self->debug
-                 ("packing sprintf() data into score!\n");
-             }
              my $gene = Bio::SeqFeature::Generic->new(-seq_id => $seqid,
                                                        -start  => $start,
--- 347,350 ----