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| − | #!/usr/bin/perl
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| − | ## Extract individual patients from the original GSK file
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| − | # we are going to use the file mapping_info.txt to map Illumina IDs with patient IDs
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| − | # input will be
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| − | use Getopt::Long;
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| − | use Data::Dumper;
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| − | use strict;
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| − | my $VERSION = '1_00';
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| − | # Check if programm called correctly
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| − | my ($fp, $outdir, $fpout);
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| − | my $result = GetOptions ("infile=s" => \$fp,
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| − | "outfile=s"=> \$fpout,
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| − | "outdir=s"=> \$outdir);
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| − | if($fp eq "" || $fpout eq "" || $outdir eq "" ){
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| − | print "usage: perl extractPatients.pl -infile <csv file with SNP data> -outdir <output directory> -outfile <output file>\n";
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| − | exit(-1);
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| − | }
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| − | open(OUTPUT2, '>', $fpout) || die("Could not open file $fpout!");
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| − | print2("#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");
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| − | print2("#Version: $VERSION\n");
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| − | #read in information about mapping between Illumina individuals and GSK individuals
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| − | # file has been created from "PGX40001_GSK_SJS_B137_29Aug2007_DNAReport.xls"
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| − | my $mapfp = 'mapping_info.txt';
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| − | open(DAT, $mapfp) || die("Could not open file $mapfp!");
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| − | my @map_data=<DAT>;
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| − | my %map;
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| − | foreach my $m (@map_data) {
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| − | if ($m =~ !/^#/) {
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| − | $m =~ /(.*)\t(.*)\n/;
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| − | $map{lc $1} = $2
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| − | }
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| − | }
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| − | close(DAT);
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| − | if (!defined %map) {
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| − | print2("%map not defined");
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| − | die("%map not defined");
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| − | }
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| − | #print Dumper(\%map);
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| − | #$ head -30 PGx40001_12278-DNA.csv
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| − | #[Header]
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| − | #BSGT Version,3.1.10
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| − | #Processing Date,8/28/2007 11:53 AM
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| − | #Content,,Human1Mv1_C.bpm
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| − | #Num SNPs,1069083
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| − | #Total SNPs,1072820
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| − | #Num Samples,94
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| − | #Total Samples,292
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| − | #[Data]
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| − | #SNP Name,Sample ID,Allele1 - Forward,Allele2 - Forward,Allele1 - AB,Allele2 - AB,X,Y,X Raw,Y Raw,GC Score
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| − | #rs758676,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.420,0.611,3306,4684,0.8100
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| − | #rs3916934,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.341,0.511,2686,3914,0.9114
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| − | #rs2711935,WG0012278-DNA_A02_2949_A02,T,T,A,A,1.033,0.030,8298,255,0.9032
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| − | #rs17126880,WG0012278-DNA_A02_2949_A02,C,C,B,B,0.031,1.178,262,9201,0.9278
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| − | #rs12831433,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.947,1.015,7620,7947,0.8485
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| − | #rs12797197,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.132,0.290,1062,2265,0.8524
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| − |
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| − | open(DAT, $fp) || die("Could not open file $fp!");
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| − |
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| − | my $header=0;
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| − | my $l = 0;
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| − | my $oldId = "empty";
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| − | while (<DAT>) {
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| − | #ignore lines until we hit "[Data]"
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| − | #then read one more line
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| − | if ($header<2) {
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| − | if (/^\[Data\]/ || $header >0) {
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| − | $header ++;
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| − | }
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| − | next;
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| − | }
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| − | $ l ++;
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| − | if (!($l % 100000)) {
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| − | print2 ("processing line $l\n");
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| − | }
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| − | my @line = split(/,/);
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| − |
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| − | if (!defined $map{lc $line[1]}) {
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| − | print2( "unknown ID: " . $map{lc $line[1]} . ":::" . $line[1] . "\n");
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| − | }
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| − | if ($oldId ne $line[1]) {
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| − | if (<OUTFILE>) {
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| − | close (OUTFILE);
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| − | }
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| − | open(OUTFILE, ">", $outdir . "/" . $map{lc $line[1]} . ".txt");
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| − | print(OUTFILE "#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");
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| − | print(OUTFILE "#Version: $VERSION\n");
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| − | }
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| − | $oldId = $line[1];
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| − | print (OUTFILE $line[0] . "\t" . $line[2] . "\t" . $line[3] . "\n");
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| − |
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| − | #print "$_";
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| − | }
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| − | close(OUTFILE);
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| − | close(OUTPUT2);
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| − | #===============================
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| − |
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| − | sub print2 {
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| − |
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| − | my ($str) = @_;
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| − | print $str ;
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| − | print(OUTPUT2 $str);
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| − | }
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