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1 : overbeek 1.1 # -*- perl -*-
2 : olson 1.2 #
3 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 : overbeek 1.1
20 :     # useage: clustal_to_fasta < ClustalAlgn > FastAseqs
21 :    
22 :     $next_id = 0;
23 :     while (defined($_ = <STDIN>))
24 :     {
25 :     @flds = split(/\s+/,$_);
26 :     if (($#flds == 1) && ($_ =~ /^[A-Za-z0-9]/))
27 :     {
28 :     if (!$line{$flds[0]})
29 :     {
30 :     $ids[$next_id++] = $flds[0];
31 :     }
32 :     $line{$flds[0]} .= $flds[1];
33 :     }
34 :     }
35 :    
36 :     for ($i=0; $i < $next_id; $i++)
37 :     {
38 :     print ">$ids[$i]\n$line{$ids[$i]}\n";
39 :     }

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