Mercurial > repos > devteam > condense_characters

annotate condense_characters.pl @ 0:5c87e8fdf38b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:24:51 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 #! /usr/bin/perl -w
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
2
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
3 use strict;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
4 use warnings;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
5
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
6 # condenses all consecutive characters of one type
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
7 # convert_characters.pl [input] [character] [output]
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
8
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
9 die "Check arguments" unless @ARGV == 3;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
10
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
11 my $inputfile = $ARGV[0];
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
12 my $character = $ARGV[1];
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
13 my $outputfile = $ARGV[2];
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
14
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
15
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
16 my $convert_from;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
17 my $convert_to;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
18
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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19
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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20 if ($character eq "s")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
22 $convert_from = '\s';
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
23 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
24 elsif ($character eq "T")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 $convert_from = '\t';
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
27 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
28 elsif ($character eq "Sp")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 $convert_from = " ";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
31 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 elsif ($character eq "Dt")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
33 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
34 $convert_from = '\.';
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
35 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
36 elsif ($character eq "C")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
37 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
38 $convert_from = ",";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
39 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
40 elsif ($character eq "D")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
41 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
42 $convert_from = "-";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
43 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
44 elsif ($character eq "U")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
45 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
46 $convert_from = "_";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
47 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
48 elsif ($character eq "P")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
49 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
50 $convert_from = '\|';
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
51 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
52 else
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
53 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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54 die "Invalid value specified for convert from\n";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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55 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
56
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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57
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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58 if ($character eq "T")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
59 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
60 $convert_to = "\t";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
61 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
62 elsif ($character eq "Sp")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
63 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
64 $convert_to = " ";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
65 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
66 elsif ($character eq "Dt")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
67 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
68 $convert_to = "\.";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
69 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
70 elsif ($character eq "C")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
71 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
72 $convert_to = ",";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
73 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
74 elsif ($character eq "D")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
75 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
76 $convert_to = "-";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
77 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
78 elsif ($character eq "U")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
79 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
80 $convert_to = "_";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
81 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
82 elsif ($character eq "P")
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
83 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
84 $convert_to = "|";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
85 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
86 else
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
87 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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88 die "Invalid value specified for Convert to\n";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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89 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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90
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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91 my $fhIn;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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92 open ($fhIn, "< $inputfile") or die "Cannot open source file";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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93
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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94 my $fhOut;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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95 open ($fhOut, "> $outputfile");
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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96
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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97 while (<$fhIn>)
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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98 {
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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99 my $thisLine = $_;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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100 chomp $thisLine;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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101 $thisLine =~ s/${convert_from}+/$convert_to/g;
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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102 print $fhOut $thisLine,"\n";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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103 }
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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104 close ($fhIn) or die "Cannot close source file";
5c87e8fdf38b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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105 close ($fhOut) or die "Cannot close output file";