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0
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1 #! /usr/bin/perl
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2
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3 die "FIMO_GFF_File\tOutput_Path\n" unless $#ARGV == 1;
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4 my($input, $output) = @ARGV;
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5 open(IN, "<$input") or die "Can't open $input for reading!\n";
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6
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7 ##gff-version 3
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8 #chr10:265210-265270(-) fimo nucleotide_motif 25 36 40.2 + . Name=1;ID=1-1-chr10:265210-265270(-);pvalue=9.48e-05;qvalue=0.00885;sequence=ACTTACCCTCAT;
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9 #chr10:295039-295099(+) fimo nucleotide_motif 25 36 55.3 + . Name=1;ID=1-1-chr10:295039-295099(+);pvalue=2.97e-06;qvalue=0.00107;sequence=TGTTACCCGTTC;
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10 #chr10:576747-576807(-) fimo nucleotide_motif 25 36 56.2 + . Name=1;ID=1-1-chr10:576747-576807(-);pvalue=2.37e-06;qvalue=0.00107;sequence=CGTTACCCGACC;
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11
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1
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12 #chr1 genetrack . 123950 123970 22 + . stddev=0.0
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13 #chr1 genetrack . 565745 565765 12 + . stddev=0.0
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14 #chr1 genetrack . 565793 565813 44 + . stddev=0.298065387468
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0
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15
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16 @COORD = ();
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17 @ID_NUM = ();
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18 $line = "";
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19 while($line = <IN>) {
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1
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20 chomp($line);
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0
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21 next if($line =~ /gff-version/);
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22 @array = split(/\t/, $line);
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23 @CHR = split(/\:/, $array[0]);
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1
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24 @gff_COORD = split(/\(/, $CHR[1]);
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25 @START_array = split(/\-/, $gff_COORD[0]);
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26 $fimo_DIR = "+";
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27 if($gff_COORD[1] =~ "-") { $fimo_DIR = "-"; }
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0
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28
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29 $DIR = $array[6];
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30 $SCORE = $array[5];
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31
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1
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32 @NAME = split(/\;/, $array[8]);
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0
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33 $NEW = 0;
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34 for($x = 0; $x <= $#ID_NUM; $x++) {
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35 if($ID_NUM[$x] eq $NAME[0]) {
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36 $NEW = 1;
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37 $x = $#ID_NUM + 1;
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38 }
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39 }
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40 if($NEW == 0) { push(@ID_NUM, $NAME[0]); }
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41
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1
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42 $START = $START_array[0] + $array[3] - 1;
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43 $STOP = $START_array[0] + $array[4] - 1;
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0
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44
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1
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45 if($fimo_DIR eq "-") {
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46 if($DIR eq "+") { $DIR = "-"; }
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47 else { $DIR = "+"; }
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48 }
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0
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49
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50 $newline = "$CHR[0]\tfimo\tmotif\t$START\t$STOP\t$SCORE\t$DIR\t.\t$CHR[0]\_$START\_$STOP\_$DIR";
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51 $EXISTS = 0;
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52 for($x = 0; $x <= $#COORD; $x++) {
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53 if($newline eq $COORD[$x]{'line'}) {
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54 $EXISTS = 1;
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55 }
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56 }
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57 if($EXISTS == 0) {
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58 push(@COORD, {chr => $CHR[0], start => $START, stop => $STOP, dir => $DIR, score =>$SCORE, id => $NAME[0], line => $newline});
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59 }
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60 }
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61 close IN;
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62 @SORT = sort { $$b{'score'} <=> $$a{'score'} } @COORD;
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63
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64 for($x = 0; $x <= $#ID_NUM; $x++) {
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1
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65 @FILENAME = split(/\=/, $ID_NUM[$x]);
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66 $FILE = "MOTIF$FILENAME[1]";
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67 open(OUT, ">$output/$FILE.gff") or die "Can't open $output/$FILE.gff for writing!\n";
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68 for($y = 0; $y <= $#SORT; $y++) {
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69 if($SORT[$y]{'id'} eq $ID_NUM[$x]) {
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70 print OUT $SORT[$y]{'line'},"\n";
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71 }
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72 }
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73 close OUT;
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0
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74 }
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