Mercurial > repos > jdv > porechop

annotate porechop_summarize.pl @ 8:852b3fe95c20 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit aa6136c5fa32b987f64bd2b0dc1f72018038b0bb
author jdv
date Fri, 20 Oct 2017 23:11:21 -0400
parents 64fcb9c72e47
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
1 #!/usr/bin/env perl
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
2
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
3 use strict;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
4 use warnings;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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5 use 5.012;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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6
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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7 my $flag = 0;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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8 my $table;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
9
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
diff changeset
10 while (my $line = <STDIN>) {
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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12 print STDERR $line;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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14 if ($line =~ /Barcode\s+Reads\s+Bases\s+File/) {
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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15 $flag = 1;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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16 }
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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17 next if (! $flag);
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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19 $table .= $line;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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21 }
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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23 $table =~ s/(^\s+|\e\[\d+m)//gms;
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64fcb9c72e47 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60-dirty
jdv
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24 pos($table) = 0;
64fcb9c72e47 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60-dirty
jdv
parents: 3
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25 $table =~ s/[ \t]+/\t/gms;
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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26 say $table;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
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28 exit;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
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