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1 #!/usr/bin/perl
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2 ########################################
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3 #### Filters peaks by p-value and width
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4 #### Perl script
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5 #######################################
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6
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7
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8 use feature qw(say);
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9
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10
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11 # ==================
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12 # Parsing Arguments
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13 # ==================
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14 #initialize to NULL
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15 my $bed_file = NULL; #bed file
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16
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17 #Parse the arguments
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18 $bed_file = $ARGV[0]; #bed file
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19 #=======================> DONE!
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20
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21
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22
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23
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24 # ========================================
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25 # Parse the bed file and extend the reads
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26 # ========================================
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27 #open the file
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28 open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!");
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29
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30 while (<DATA>) {
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31 my ($chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit, $minpeak, $geom) = split(/\t/,$_,12);
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32
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33 my $size = $end - $start;
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34
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35 if($size >= $minpeak) {
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36 if($signal > $geom) {
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37 #Now write the new line
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38 $summit =~ s/\015?\012?$//;
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39 say join "\t", $chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit;
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40 }
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41 }
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42 }
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43 #=======================> DONE!
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