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revision 1.45, Mon Mar 2 22:31:33 2009 UTC revision 1.46, Sat Mar 7 18:07:36 2009 UTC
# Line 943  Line 943 
943      Trace("FASTA desired type is $desiredType.") if T(4);      Trace("FASTA desired type is $desiredType.") if T(4);
944      # Check for a feature specification. The smoking gun for that is a vertical bar.      # Check for a feature specification. The smoking gun for that is a vertical bar.
945      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
946          # Here we have a feature ID in $1. We'll need the Sprout object to process          # Here we have a feature ID in $1. We'll need a Sprout object to process it.
         # it.  
947          my $fid = $1;          my $fid = $1;
948          Trace("Feature ID for fasta is $fid.") if T(3);          Trace("Feature ID for fasta is $fid.") if T(3);
949          my $sprout = $self->DB();          my $sprout = $self->DB();
# Line 1030  Line 1029 
1029          if ($desiredType !~ /pattern/i) {          if ($desiredType !~ /pattern/i) {
1030              $fastaData =~ s/\n//g;              $fastaData =~ s/\n//g;
1031              $fastaData =~ s/\s+//g;              $fastaData =~ s/\s+//g;
1032                $fastaData =~ s/\d+//g;
1033          }          }
1034          # Finally, verify that it's DNA if we're doing DNA stuff.          # Finally, verify that it's DNA if we're doing DNA stuff.
1035          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {

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