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1 #!/usr/bin/perl
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2 # Compute gEUMA for each gene from the gUtable file and insertlendis file and print out only genes whose gEUMA is larger than 0.
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3
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4 if(@ARGV<3) { print "usage: $0 gUtable_file insertlendis_file READLENGTH\n"; exit; }
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5
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6 my ($gUtable_file,$insertlendis_file,$READLENGTH) = @ARGV;
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7
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8
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9 my $totalfreq=0;
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10 open LENDIS, $insertlendis_file or die "Can't open insertlendis file $insertlendis_file\n";
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11 while(<LENDIS>){
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12 chomp;
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13 my ($insert_size, $freq) = split/\t/;
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14 $insertlendis{"$insert_size"}=$freq;
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15 $totalfreq+=$freq;
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16 }
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17 close LENDIS;
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18
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19
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20
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21 print "gene\tgEUMA\n"; #header
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22 open GUTABLE, $gUtable_file or die "Can't open gUtable file $gUtable_file\n";
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23 chomp($header = <GUTABLE>);
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24 @distances = split/\t/,$header;
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25 shift @distances; #'gene'
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26 while(<GUTABLE>){
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27 chomp;
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28 my @line = split/\t/;
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29 my $gene = shift @line;
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30 my $EUMA=0;
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31 for my $i (0..$#distances){
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32 $d=$distances[$i];
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33 $pUMA = $line[$i] * ($insertlendis{$d}/$totalfreq) ;
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34 $EUMA += $pUMA;
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35 }
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36 if($EUMA>=0.005) { printf "$gene\t%.2f\n",$EUMA; } # use >=0.005 instead of >0, because I'm plotting two decimals after point. (in bp)
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37 }
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38 close GUTABLE;
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39
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40
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41
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