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1 : olson 1.2 #
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 : efrank 1.1 # usage: generate_input_for_auto_assignments < fasta > ready.for.auto.assign
19 :    
20 :     use FIG;
21 :    
22 :     $/ = "\n>";
23 :     while (defined($_ = <STDIN>))
24 :     {
25 :     chomp;
26 :     if ($_ =~ /^>?(\S+)([^\n]*\n)(.*)/s)
27 :     {
28 :     $id = $1;
29 :     $comment = $2;
30 :     $seq = $3;
31 :     $seq =~ s/\s//g;
32 :     print "$id\t$seq\n";
33 :     }
34 :     else
35 :     {
36 :     print STDERR "ERROR: $id\n";
37 :     }
38 :     }

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