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revision 1.9, Wed Sep 10 22:19:38 2008 UTC revision 1.10, Mon Nov 24 13:17:38 2008 UTC
# Line 46  Line 46 
46  my $trouble = 0;  my $trouble = 0;
47  for (my $arg=$#ARGV; ($arg >= 0); $arg--)  for (my $arg=$#ARGV; ($arg >= 0); $arg--)
48  {  {
49      if ($ARGV[$arg] =~ m/^-{1,2}code=(\d+)/) {      if ($ARGV[$arg] =~ m/^-{1,2}help/) {
50            warn "\n\tusage: $usage\n\n";
51            exit(0);
52        }
53        elsif ($ARGV[$arg] =~ m/^-{1,2}code=(\d+)/) {
54          $genetic_code = $1;          $genetic_code = $1;
55          splice(@ARGV, $arg, 1);          splice(@ARGV, $arg, 1);
56      }      }
# Line 158  Line 162 
162      my %len_of;     #...Hash storing training contig lens      my %len_of;     #...Hash storing training contig lens
163      while (($contig_id, $seqP) = &read_fasta_record(\*CONTIGS))      while (($contig_id, $seqP) = &read_fasta_record(\*CONTIGS))
164      {      {
165          $len_of{$contig_id} = length($$seqP);          my $len = $len_of{$contig_id} = length($$seqP);
166    
167          open( TMP, ">$tmp_contig") || die "Could not write-open $tmp_contig";          open( TMP, ">$tmp_contig") || die "Could not write-open $tmp_contig";
168          &display_id_and_seq($contig_id, $seqP, \*TMP);          &display_id_and_seq($contig_id, $seqP, \*TMP);
169          close(TMP) || die "Could not close $tmp_contig";          close(TMP) || die "Could not close $tmp_contig";
170    
171            if ($len >= 1000) {
172          print STDERR "\nScanning contig $contig_id for long orfs\n" if $ENV{VERBOSE};          print STDERR "\nScanning contig $contig_id for long orfs\n" if $ENV{VERBOSE};
173            }
174            else {
175                print STDERR "\nSkipping contig $contig_id --- too short (len=$len)\n" if $ENV{VERBOSE};
176                next;
177            }
178    
179          system("$glimmer_bin/long-orfs -l -n -t 1.15 $genetic_code_switch  $tmp_contig $tmp_coords")          system("$glimmer_bin/long-orfs -l -n -t 1.15 $genetic_code_switch  $tmp_contig $tmp_coords")
180              && die "Could not extract training ORFs from contig $contig_id";              && die "Could not extract training ORFs from contig $contig_id";

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