[Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.113,1.114

Christopher John Fields cjfields at dev.open-bio.org
Thu Mar 22 15:14:11 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO
In directory dev.open-bio.org:/tmp/cvs-serv18350

Modified Files:
	blast.pm 
Log Message:
bug 2246 tentative fix

Index: blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blast.pm,v
retrieving revision 1.113
retrieving revision 1.114
diff -C2 -d -r1.113 -r1.114
*** blast.pm	1 Feb 2007 20:02:09 -0000	1.113
--- blast.pm	22 Mar 2007 19:14:08 -0000	1.114
***************
*** 593,596 ****
--- 593,598 ----
                  $self->_start_iteration;
              }
+             # these elements are dropped with some multiquery reports; add
+             # back here
              $self->element(
                  {
***************
*** 614,618 ****
              while ( defined( $_ = $self->_readline() ) ) {
                  
!                 if (/(?<!cor)([\d\.\+\-eE]+)\s+([\d\.\+\-eE]+)(\s+\d+)?\s*$/) {
  
                      # the last match is for gapped BLAST output
--- 616,620 ----
              while ( defined( $_ = $self->_readline() ) ) {
                  
!                 if (/(?<!cor)(\d[\d\.\+\-eE]+)\s+((?:\d|e)[\d\.\+\-eE]+)(\s+\d+)?\s*$/xms) {
  
                      # the last match is for gapped BLAST output
***************
*** 770,774 ****
                  }
              );
!             my ( $acc, $version ) = &_get_accession_version($id);
              $self->element(
                  {
--- 772,776 ----
                  }
              );
!             my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id);
              $self->element(
                  {
***************
*** 777,786 ****
                  }
              );
!  
              # add hit significance (from the hit table)
              # this is where Bug 1986 goes awry
              
              my $v = shift @hit_signifs;
              if ( defined $v ) {
                  $self->element(
                      {
--- 779,797 ----
                  }
              );
!             $self->element(
!                 {
!                     'Name' => 'Hit_gi',
!                     'Data' => $gi
!                 }
!             ) if $gi; 
              # add hit significance (from the hit table)
              # this is where Bug 1986 goes awry
              
              my $v = shift @hit_signifs;
+                     
              if ( defined $v ) {
+                 # should perform a sanity check here,
+                 # but that breaks some report parsing.  Needs investigation
+                 
                  $self->element(
                      {



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