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revision 1.159, Fri Sep 24 18:58:42 2004 UTC revision 1.160, Fri Sep 24 20:27:22 2004 UTC
# Line 2518  Line 2518 
2518                  while (<$fh>)                  while (<$fh>)
2519                  {                  {
2520                      chomp;                      chomp;
2521                      if (s/^\s*(\S+)([^\n]*)\n//)  
2522                        #
2523                        # Pull the contig identifier from the first line.
2524                        # We need the >? to handle the first line in the file;
2525                        # the others are removed by the chomp above because
2526                        # $/ is set to "\n>";
2527                        #
2528    
2529                        if (s/^>?\s*(\S+)([^\n]*)\n//)
2530                      {                      {
2531                          my $ident = $1;                          my $ident = $1;
2532                          my $contig_txt = $_;                          my $contig_txt = $_;
# Line 6759  Line 6767 
6767      return $tran_peg;      return $tran_peg;
6768  }  }
6769    
6770    =pod
6771    
6772    =head1 tough_search($pegs, $seq_of, $tran_peg, $sought)
6773    
6774    $pegs - not used
6775    $seq_of - hash from peg to peg sequence
6776    $tran_peg - hash into which translated pegs are placed
6777    $sought - hash keyed on the list of pegs we're looking for.
6778    
6779    =cut
6780    
6781  sub tough_search {  sub tough_search {
6782      my($self,$pegs,$seq_of,$tran_peg,$sought) = @_;      my($self,$pegs,$seq_of,$tran_peg,$sought) = @_;
6783      my($peg,$seq,%needH,%needT,%poss,$id,$sub,$to,$x,$genome);      my($peg,$seq,%needH,%needT,%poss,$id,$sub,$to,$x,$genome);

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