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1 #!/usr/bin/perl
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2 # Compute iEUMA for each isoform from the iUtable file and insertlendis file and print out only isoforms whose iEUMA is larger than 0.
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3
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4 if(@ARGV<2) { print "usage: $0 iUtable_file insertlendis_file READLENGTH\n"; exit; }
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5
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6 my ($iUtable_file,$insertlendis_file,$READLENGTH) = @ARGV;
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7
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8 open IUTABLE, $iUtable_file or die "Can't open iUtable file $iUtable_file\n";
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9 chomp($header = <IUTABLE>);
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10 @distances = split/\t/,$header;
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11 shift @distances; #'gene'
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12 while(<IUTABLE>){
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13 chomp;
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14 my @line = split/\t/;
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15 my $gid = shift @line;
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16 my $transcript = shift @line;
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17 my $gene = "$gid\t$transcript";
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18 for my $i (0..$#distances){
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19 $iUtable{$gene}{"$distances[$i]"}=$line[$i];
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20 }
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21 }
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22 close IUTABLE;
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23
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24
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25 my $totalfreq=0;
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26 open LENDIS, $insertlendis_file or die "Can't open insertlendis file $insertlendis_file\n";
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27 while(<LENDIS>){
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28 chomp;
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29 my ($insert_size, $freq) = split/\t/;
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30 $insertlendis{$insert_size}=$freq;
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31 $totalfreq+=$freq;
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32 }
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33 close LENDIS;
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34
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35 print "gene\ttranscript\tiEUMA\n"; #header
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36 for my $gene (sort keys %iUtable){
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37 my $EUMA=0;
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38 for my $d (keys %{$iUtable{$gene}}){
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39 $pUMA = $iUtable{$gene}{$d} * ($insertlendis{$d}/$totalfreq) ;
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40 $EUMA += $pUMA;
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41 }
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42 if($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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43 }
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44
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