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1 #!/usr/bin/perl
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2
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3 # write bowtie output to bed file
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4
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5 # perl bowtie2bed.pl s_5_trimmed.map outputfile 200
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6 # input
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7 # inputfile
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8 # extension
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9
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10 $inputfile = $ARGV[0];
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11 $extension = $ARGV[2];
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12 $outputfile = $ARGV[1];#$inputfile.".extended_$extension"."bp.bed";
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13
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14 print "input file: $inputfile\n";
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15 print "output file: $outputfile\n";
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16 print "track name: $outputfile\n";
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17
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18 open (IN,$inputfile) or die $!;
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19 open (OUT,">$outputfile") or die $!;
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20
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21 print OUT "track name=$outputfile itemRgb=On\n";
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22
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23 while(<IN>)
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24 {
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25 @flds = split/\t/;
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26 $flds[0] =~ s/ /-/g;#substitute space to dash
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27
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28 if ($flds[1] eq "+")
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29 {
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30 print OUT join("\t",$flds[2],$flds[3],$flds[3]+$extension+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"255,0,0","\n");
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31 }
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32 else
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33 {
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34
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35 print OUT join("\t",$flds[2],max(0,$flds[3]-$extension),$flds[3]+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"0,255,0","\n");
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36 }
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37 }
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38 close(IN);
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39 close(OUT);
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40
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41 sub max()
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42 {
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43 ($a,$b) = @_;
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44 return $a>$b?$a:$b;
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45 }
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