Mercurial > repos > jdv > porechop

annotate porechop_summarize.pl @ 10:0cb1ba651e9e draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 83364d7d78ca5524a08065daef995bfcd54a379d-dirty
author jdv
date Fri, 01 Dec 2017 21:36:54 -0500
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:
diff changeset
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
parents:
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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:
diff changeset
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 $line;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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13
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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14 if ($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:
diff changeset
15 $flag = 1;
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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16 }
80408ff0c1f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
jdv
parents:
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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
parents:
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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
parents:
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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
parents: 3
diff changeset
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
parents:
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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
parents:
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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
jdv
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