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Fixed chromosome comparison in createNormalizedCoverageFiles() #40

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Fixed chromosome comparison in createNormalizedCoverageFiles() #40

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11bbbf5
Fixed chromosome comparison in createNormalizedCoverageFiles()
Mar 4, 2019
4356b02
Merge pull request #1 from ryim/ryim-patch-1
Mar 4, 2019
70e696f
Stopped deleting raw output in startWithBestScore(), added autoMean a…
Jul 15, 2019
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10 changes: 5 additions & 5 deletions CoNVaDING.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -961,7 +961,7 @@ sub startWithBestScore{
push(@NORMTOTAL, $refNormTotal);
push(@NORMGENE, $refNormGene);
#Finalize header line for outputfile
my $lin = "AUTO_RATIO\tAUTO_ZSCORE\tAUTO_VC\tGENE_RATIO\tGENE_ZSCORE\tGENE_VC\tSHAPIRO-WILK\n";
my $lin = "AUTO_RATIO\tAUTO_ZSCORE\tAUTO_VC\tAUTO_MEAN\tAUTO_SD\tGENE_RATIO\tGENE_ZSCORE\tGENE_VC\tSHAPIRO-WILK\n";
$outputToWrite .= $lin; #concatenate full generated line to files

#Iterate over controlfiles and put into array of arrays
Expand Down Expand Up @@ -1027,9 +1027,9 @@ sub startWithBestScore{

$lin = $controlChr[$i] . "\t" . $controlStart[$i] . "\t" . $controlStop[$i] . "\t" . $controlGene[$i] . "\t$sampleValue\t";
$outputToWrite .= $lin; #concatenate full generated line to files
$lin = "$autoRatio\t$autoZscore\t$autoVc\t";
$lin = "$autoRatio\t$autoZscore\t$autoVc\t$autoMean\t$autoSD\t";
$outputToWrite .= $lin; #concatenate full generated line to files

my $TNsi = $NORMGENE[0]->[$i];
calcMeanSD(\@TNciArray);
undef(@TNciArray);
Expand Down Expand Up @@ -1234,7 +1234,7 @@ sub createOutputLists{
open(BESTSCORE, "$outputdir/$outputPostfixRemoved.best.score.txt") or die("Unable to open file: $!"); #Read best match file
my @bestScoreFile= <BESTSCORE>;
close(BESTSCORE);
`rm $outputdir/$outputPostfixRemoved.best.score.txt`; #Remove *.best.score.txt file, since it is almost the same as other files produced
# `rm $outputdir/$outputPostfixRemoved.best.score.txt`; #Remove *.best.score.txt file, since it is almost the same as other files produced
my @targets;
my @genes;
my @values;
Expand Down Expand Up @@ -2104,7 +2104,7 @@ sub createNormalizedCoverageFiles {
my $normautoControl=$linesControl[$normAutoIdxControl];
my $normsexControl=$linesControl[$normSexIdxControl];
my $keyControl = $lineControl;
if ($chrSample == $chrControl && $startSample == $startControl && $stopSample == $stopControl){ #Check if chr, start and stop match, if not throw error and skip this file from analysis
if ($chrSample eq $chrControl && $startSample == $startControl && $stopSample == $stopControl){ #Check if chr, start and stop match, if not throw error and skip this file from analysis
my $absDiffAuto = abs($normautoSample-$normautoControl); #Calculate absolute difference autosomal coverage
my $absDiffSex = abs($normsexSample-$normsexControl); #Calculate absolute difference all coverage
push(@absDiffsAuto, $absDiffAuto);
Expand Down