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revision 1.17, Thu Sep 29 18:59:01 2005 UTC revision 1.20, Mon Dec 5 19:06:30 2005 UTC
# Line 1  Line 1 
1  #  #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18    #
19  # FIG GFF utilities.  # FIG GFF utilities.
20  #  #
21    
# Line 393  Line 410 
410                  chomp($addseq);                  chomp($addseq);
411                  $fastasequences .= ">$protein_id\n$addseq\n";                  $fastasequences .= ">$protein_id\n$addseq\n";
412    
413                  my $addseq = uc($fig->dna_seq($genome, @location));                  $addseq = uc($fig->dna_seq($genome, @location));
414                  $addseq =~ s/(.{$linelength})/$1\n/g; chomp($addseq);                  $addseq =~ s/(.{$linelength})/$1\n/g; chomp($addseq);
415    
416                  $fastasequences .= ">$cds_id\n$addseq\n";                  $fastasequences .= ">$cds_id\n$addseq\n";
# Line 878  Line 895 
895      my($self, $fh, $first_line) = @_;      my($self, $fh, $first_line) = @_;
896      my($cur, $cur_id);      my($cur, $cur_id);
897    
898      for ($_ = $first_line; $_;  $_ = <$fh>, chomp)      for ($_ = $first_line; defined($_);  $_ = <$fh>, chomp)
899      {      {
900          if (/^>\s*(\S+)/)          if (/^>\s*(\S+)/)
901          {          {

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