[Bioperl-guts-l] bioperl-live/Bio/SearchIO infernal.pm,1.1,1.2

Christopher John Fields cjfields at dev.open-bio.org
Sat Feb 17 00:21:01 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO
In directory dev.open-bio.org:/tmp/cvs-serv4705/Bio/SearchIO

Modified Files:
	infernal.pm 
Log Message:
infernal parsing fixes

Index: infernal.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/infernal.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** infernal.pm	4 Feb 2007 05:06:30 -0000	1.1
--- infernal.pm	17 Feb 2007 05:20:59 -0000	1.2
***************
*** 228,236 ****
      while ( defined( $line = $self->_readline ) ) {
          next if $line =~ m{^\s+$};
!         if ($line =~ m{^CPU\stime}xms ) {
!             if (index($line, 'band calc') > 0) {
!                 $version = 0.71 ;
!             }
!         } elsif ($line =~ m{^sequence:\s+(\S+)} ){
              if (!$self->within_element('result')) {
                  $seentop = 1;
--- 228,234 ----
      while ( defined( $line = $self->_readline ) ) {
          next if $line =~ m{^\s+$};
!         # bypass this for now...
!         next if $line =~ m{^HMM\shit};
!         if ($line =~ m{^sequence:\s+(\S+)} ){
              if (!$self->within_element('result')) {
                  $seentop = 1;
***************
*** 314,318 ****
                  chomp $line;
                  # exit loop if at end of file or upon next hit/HSP
!                 if (!defined($line) || $line =~ m{^(sequence|hit|CPU)}) {
                      $self->_pushback($line);
                      last HSP;
--- 312,316 ----
                  chomp $line;
                  # exit loop if at end of file or upon next hit/HSP
!                 if (!defined($line) || $line =~ m{^\S+}) {
                      $self->_pushback($line);
                      last HSP;



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