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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 open GUTABLE, $gUtable_file or die "Can't open gUtable file $gUtable_file\n";
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9 chomp($header = <GUTABLE>);
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10 @distances = split/\t/,$header;
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11 shift @distances; #'gene'
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12 while(<GUTABLE>){
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13 chomp;
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14 my @line = split/\t/;
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15 my $gene = shift @line;
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16 for my $i (0..$#distances){
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17 $gUtable{$gene}{"$distances[$i]"}=$line[$i];
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18 }
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19 }
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20 close GUTABLE;
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21
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22
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23 my $totalfreq=0;
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24 open LENDIS, $insertlendis_file or die "Can't open insertlendis file $insertlendis_file\n";
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25 while(<LENDIS>){
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26 chomp;
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27 my ($insert_size, $freq) = split/\t/;
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28 $insertlendis{"$insert_size"}=$freq;
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29 $totalfreq+=$freq;
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30 }
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31 close LENDIS;
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32
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33 print "gene\tgEUMA\n"; #header
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34 for my $gene (sort keys %gUtable){
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35 my $EUMA=0;
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36 for my $d (keys %{$gUtable{$gene}}){
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37 $pUMA = $gUtable{$gene}{$d} * ($insertlendis{$d}/$totalfreq) ;
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38 $EUMA += $pUMA;
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39 }
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40 if($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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41 }
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42
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