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1 ########################################################################
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2 # JAMMv1.0.7rev1 is a peak finder for joint analysis of NGS replicates.
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3 # Copyright (C) 2014-2015 Mahmoud Ibrahim
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your 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,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 #
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18 # Contact: mahmoud.ibrahim@mdc-berlin.de
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19 ########################################################################
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0
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20
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21
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22 use feature qw(say);
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23
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24
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25 # ==================
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26 # Parsing Arguments
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27 # ==================
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28 #initialize to NULL
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29 my $bed_file = NULL; #bed file
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30
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31 #Parse the arguments
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32 $bed_file = $ARGV[0]; #bed file
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33 #=======================> DONE!
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34
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35
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36
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37
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38 # ========================================
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39 # Parse the bed file and extend the reads
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40 # ========================================
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41 #open the file
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42 open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!");
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43
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44 while (<DATA>) {
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45 my ($chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit, $minpeak, $geom) = split(/\t/,$_,12);
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46
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47 my $size = $end - $start;
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48
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49 if($size >= $minpeak) {
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50 if($signal > $geom) {
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51 #Now write the new line
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52 $summit =~ s/\015?\012?$//;
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53 say join "\t", $chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit;
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54 }
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55 }
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56 }
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57 #=======================> DONE!
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