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revision 1.7, Wed Oct 10 20:50:55 2007 UTC revision 1.10, Wed Nov 5 22:39:29 2008 UTC
# Line 65  Line 65 
65  }  }
66    
67  #  #
68    # Determine genetic code.
69    #
70    
71    my $genetic_code = $meta->get_metadata("genome.genetic_code");
72    if (!defined($genetic_code))
73    {
74        $meta->add_log_entry("Genetic code not defined; defaulting to 11");
75        $genetic_code = 11;
76    }
77    
78    #
79  # Reformat and split.  # Reformat and split.
80  #  #
81  # Only do this if we are doing gene calling.  # Only do this if we are doing gene calling.
# Line 73  Line 84 
84  my $formatted = "$raw_dir/contigs";  my $formatted = "$raw_dir/contigs";
85  my @cmd;  my @cmd;
86    
87    my $split_size = 3;
88    if ($FIG_Config::rast_contig_ambig_split_size =~ /^\d+$/)
89    {
90        $split_size = $FIG_Config::rast_contig_ambig_split_size;
91    }
92    
93  if ($keep_genecalls)  if ($keep_genecalls)
94  {  {
95      my $reformat_log = "$errdir/reformat_contigs.stderr";      my $reformat_log = "$errdir/reformat_contigs.stderr";
# Line 83  Line 100 
100  {  {
101      my $reformat_split_log = "$errdir/reformat_contigs_split.stderr";      my $reformat_split_log = "$errdir/reformat_contigs_split.stderr";
102    
103      @cmd = ("$FIG_Config::bin/reformat_contigs", "-v", "-logfile=$reformat_split_log", "-split", $unformatted, $formatted);      @cmd = ("$FIG_Config::bin/reformat_contigs", "-v", "-logfile=$reformat_split_log", "-split=$split_size", $unformatted, $formatted);
104  }  }
105    
106  print "Run @cmd\n";  print "Run @cmd\n";
# Line 119  Line 136 
136    
137  @cmd = ("$FIG_Config::bin/rapid_propagation", "--errdir", $errdir,  @cmd = ("$FIG_Config::bin/rapid_propagation", "--errdir", $errdir,
138          @keep_genecalls_flag,          @keep_genecalls_flag,
139            "--code", $genetic_code,
140          "--meta", $meta_file,          "--meta", $meta_file,
141          "--tmpdir", $tmpdir,          "--tmpdir", $tmpdir,
142          $raw_dir, $rp_dir);          $raw_dir, $rp_dir);

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