Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/gff2bed_v2.pl @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #! /usr/bin/perl
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
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4 #
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5 # This program is free software; ; you can redistribute it and/or modify
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 # it under the terms of the GNU Lesser General Public License as published by
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 # the Free Software Foundation; either version 3 of the License, or (at your
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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8 # option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 # GNU General Public License for more details.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 $fname=$ARGV[0]; #legge il nome del file che gli passi dopo il comando
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17 $col3=$ARGV[1];
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 qx {sort -k 1,1 -k 4,4n $fname >$fname.sortato};
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 open(FILE, "< $fname.sortato") or die "Cannot find file $fname\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 @array=<FILE>;
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25 print "track type=wiggle_0 name=\"$col3\" description=\"raw_data ratio\" visibility=full autoscale=off maxHeightPixels=100:50:20 color=200,100,0 altColor=0,100,200 \n";
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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27 for ($i=0;$i<$#array;$i++){
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28 @array_new= split("\t",$array[$i]);
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29 @array_new2=split("\t",$array[$i+1]);
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30 $dist=$array_new[4]-$array_new2[3];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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31 if (($array_new[4]>=$array_new2[3])&&("$array_new[0]"eq"$array_new2[0]")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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32 $fine=$array_new2[3]-1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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33 }
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34 else {
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35 $fine=$array_new[4];
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36
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37 }
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38 print "$array_new[0]\t$array_new[3]\t$fine\t$array_new[5]\n";
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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40 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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41 @array_fine=split("\t", $array[$#array]);
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42 print "$array_fine[0]\t$array_fine[3]\t$array_fine[4]\t$array_fine[5]\n";
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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44 close FILE;