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revision 1.6, Mon Aug 27 21:41:48 2012 UTC revision 1.7, Thu Sep 19 19:09:49 2013 UTC
# Line 1  Line 1 
1  # -*- perl -*-  # -*- perl -*-
2  ########################################################################  ########################################################################
3  # Copyright (c) 2003-2009 University of Chicago and Fellowship  # Copyright (c) 2003-2013 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
6  # This file is part of the SEED Toolkit.  # This file is part of the SEED Toolkit.
# Line 29  Line 29 
29    
30  Options:  Options:
31    
32      -a 'role'  #  Proposed assignment; empty string supresses the field      -a 'role'  #  Proposed assignment; empty string supresses the output field
                #    (D = 'SSU rRNA ## 16S rRNA, small subunit ribosomal RNA')  
33      -b         #  Add a blank line between genomes (D = no blank)      -b         #  Add a blank line between genomes (D = no blank)
34      -c nt      #  Condense the sequence to first and last nt nucleotides (D = full seq)      -c nt      #  Condense the sequence to first and last nt nucleotides (D = full seq)
35      -e dist    #  Maximum nucleotides at end to extrapolate a match (D = 10)      -e dist    #  Maximum nucleotides at end to extrapolate a match (D = 10)
# Line 38  Line 37 
37      -s         #  Do not show sequence      -s         #  Do not show sequence
38      -t 'tag'   #  A short tage to identify the nature of the feature; allows      -t 'tag'   #  A short tage to identify the nature of the feature; allows
39                 #    mixing of different types; empty string supresses the field                 #    mixing of different types; empty string supresses the field
                #    (D = 'SSU_rRNA')  
40    
41  End_of_Usage  End_of_Usage
42    
# Line 54  Line 52 
52  my $tag;  my $tag;
53  my @rna;  my @rna;
54    
55  use SSU_rRNA_reps;  #  This is the module name. The package name in the module is RNA_reps. Other
56    #  modules use the same internal package structure.
57    
58    use RNA_reps_SSU_rRNA;
59  @rna        = @RNA_reps::RNA_reps;  @rna        = @RNA_reps::RNA_reps;
60  $assignment = $RNA_reps::assignment if $RNA_reps::assignment;  $assignment = $RNA_reps::assignment if $RNA_reps::assignment;
61  $tag        = $RNA_reps::tag        if $RNA_reps::tag;  $tag        = $RNA_reps::tag        if $RNA_reps::tag;

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