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Modifs ar #14

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Modifs ar #14

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d4888e0
Change pair to Y for -p argument hotspot.pl
SixEl27 Feb 24, 2017
56db1e0
Remove "" auround None paramter (option -i)
SixEl27 Mar 13, 2017
8fbe949
Replace by mutspecHotspot.xml
SixEl27 Mar 13, 2017
3a01a90
Merge pull request #13 from IARCbioinfo/master
SixEl27 Mar 15, 2017
81e6578
Correct HEADER and reading of input file
SixEl27 Jun 7, 2017
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38 changes: 25 additions & 13 deletions hotspot.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,6 @@ sub do_help {
}


my $fileformat; #Format of the input VCF/tabular variants files
my @Files; #Table of path of the input VCF/tabular variants files
my $InfoFile; #Path of tabular file containing name of input VCF/tabular variants files
my $check; #Provide the information of why the infofile is wrong, or in case of rigth, it's a hash of the series contain in the file --> become $serie variable
Expand Down Expand Up @@ -131,7 +130,7 @@ sub do_help {
"mutect2" => \@mutect2,
"mutect" => \@mutect,
"vcf" => \@vcf,
"cosmic" => \@vcf,
"cosmic" => \@cosmic,
"icgc" => \@icgc,
"tcga" => \@tcga,
"ionTorrent" => \@ionTorrent,
Expand Down Expand Up @@ -374,7 +373,7 @@ sub HotSpotv{
}
if($type!~/^Normal-Tumor-Duplicates$/){ #All the case without case with duplicates
foreach my $c (@ordcat){ #Foreach ordered categries name
$headfinal.="\t".$c."_count\t".$c."_freq %\t".$c."_Sample"; #Add the future column in the header
$headfinal.="\t".$c."_count\t".$c."_freq\t".$c."_Sample"; #Add the future column in the header
}
}
else{ #Case normal-tumor-duplicate
Expand All @@ -383,7 +382,7 @@ sub HotSpotv{
if($c eq $header[$#header]){ #$header[$#header] eq "Duplicates" --> If duplicates next because considers as the tumor
next;
}
$headfinal.="\t".$c."_count\t".$c."_freq %\t".$c."_Sample";
$headfinal.="\t".$c."_count\t".$c."_freq\t".$c."_Sample";
}
}

Expand Down Expand Up @@ -1034,10 +1033,12 @@ sub GetVar{
my $vcfheader=""; #Correspond to the header if vcf input file
my $som =-1; #Correspond to column judgment of somatic or not by the variant caller in case of mutect and mutect 2
my $first = -1;
my ( $chr)="";
my ($pos)="";
my ($ref)="";
my ($alt)="";
my $chr="";
my $pos="";
my $ref="";
my $alt="";
my %fileformat=();
my $finalformat="";
while ( defined( my $line = <IN> ) ) {
chomp($line);
if ( $line !~ /^##/ ) {
Expand All @@ -1047,6 +1048,10 @@ sub GetVar{
$header=$line;
chomp($header);
foreach my $k (keys %acceptedformat){
$chr="";
$pos="";
$ref="";
$alt="";
for ( my $i = 0 ; $i <= $#data ; $i++ ) {
if($data[$i]=~/^${$acceptedformat{$k}}[0]$/){
$chr=$i;
Expand All @@ -1072,16 +1077,22 @@ sub GetVar{
}
}
if($chr ne "" && $pos ne "" && $ref ne "" && $alt ne ""){
#print $k."\n";
$fileformat=$k;
push(@filesformat,$fileformat);
last;
$fileformat{$k}=($chr+$pos+$ref+$alt);
}
}
if(!(defined($fileformat))){
if((scalar(keys %fileformat))<=0){
print "Err : Incorrect input file format. Please refer to the documentation\n";
exit;
}
else{
my $tmp=1000;
foreach my $k (keys %fileformat){
if($fileformat{$k}<=$tmp){
$tmp=$fileformat{$k};
$finalformat=$k;
}
}
}
}
else {
if($data[$chr]!~/^chr/i){
Expand Down Expand Up @@ -1109,6 +1120,7 @@ sub GetVar{
}
}
close(IN);
push(@filesformat,$finalformat);
return($header);
}

Expand Down