Bjagla at 19:32, 18 October 2007

2007-10-18T19:32:34Z

Bjagla at 19:07, 18 October 2007

2007-10-18T19:07:30Z

New page

#!/usr/bin/perl
## Extract individual patients from the original GSK file
# we are going to use the file mapping_info.txt to map Illumina IDs with patient IDs
# input will be

use Getopt::Long;
use Data::Dumper;
use strict;

my $VERSION = '1_00';

# Check if programm called correctly

my ($fp, $outdir, $fpout);
my $result = GetOptions ("infile=s" => \$fp,
"outfile=s"=> \$fpout,
"outdir=s"=> \$outdir);
if($fp eq "" || $fpout eq "" || $outdir eq "" ){
print "usage: perl extractPatients.pl -infile <csv file with SNP data> -outdir <output directory> -outfile <output file>\n";
exit(-1);
}

open(OUTPUT2, '>', $fpout) || die("Could not open file $fpout!");
print2("#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");
print2("#Version: $VERSION\n");

#read in information about mapping between Illumina individuals and GSK individuals
# file has been created from "PGX40001_GSK_SJS_B137_29Aug2007_DNAReport.xls"

my $mapfp = 'mapping_info.txt';
open(DAT, $mapfp) || die("Could not open file $mapfp!");
my @map_data=<DAT>;
my %map;
foreach my $m (@map_data) {
if ($m =~ !/^#/) {
$m =~ /(.*)\t(.*)\n/;
$map{lc $1} = $2
}
}
close(DAT);
if (!defined %map) {
print2("%map not defined");
die("%map not defined");
}
#print Dumper(\%map);

#$ head -30 PGx40001_12278-DNA.csv
#[Header]
#BSGT Version,3.1.10
#Processing Date,8/28/2007 11:53 AM
#Content,,Human1Mv1_C.bpm
#Num SNPs,1069083
#Total SNPs,1072820
#Num Samples,94
#Total Samples,292
#[Data]
#SNP Name,Sample ID,Allele1 - Forward,Allele2 - Forward,Allele1 - AB,Allele2 - AB,X,Y,X Raw,Y Raw,GC Score
#rs758676,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.420,0.611,3306,4684,0.8100
#rs3916934,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.341,0.511,2686,3914,0.9114
#rs2711935,WG0012278-DNA_A02_2949_A02,T,T,A,A,1.033,0.030,8298,255,0.9032
#rs17126880,WG0012278-DNA_A02_2949_A02,C,C,B,B,0.031,1.178,262,9201,0.9278
#rs12831433,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.947,1.015,7620,7947,0.8485
#rs12797197,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.132,0.290,1062,2265,0.8524

open(DAT, $fp) || die("Could not open file $fp!");

my $header=0;
my $l = 0;
my $oldId = "empty";

while (<DAT>) {
#ignore lines until we hit "[Data]"
#then read one more line
if ($header<2) {
if (/^\[Data\]/ || $header >0) {
$header ++;
}
next;
}
$ l ++;
if (!($l % 100000)) {
print2 ("processing line $l\n");
}
my @line = split(/,/);

if (!defined $map{lc $line[1]}) {
print2( "unknown ID: " . $map{lc $line[1]} . ":::" . $line[1] . "\n");
}
if ($oldId ne $line[1]) {
if (<OUTFILE>) {
close (OUTFILE);
}
open(OUTFILE, ">", $outdir . "/" . $map{lc $line[1]} . ".txt");
print(OUTFILE "#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");
print(OUTFILE "#Version: $VERSION\n");

}
$oldId = $line[1];

print (OUTFILE $line[0] . "\t" . $line[2] . "\t" . $line[3] . "\n");

#print "$_";
}
close(OUTFILE);
close(OUTPUT2);
#===============================

sub print2 {

my ($str) = @_;
print $str ;
print(OUTPUT2 $str);
}

← Older revision		Revision as of 19:32, 18 October 2007
Line 1:		Line 1:
−	~~#!/usr/bin/perl~~	+
−	~~## Extract individual patients from the original GSK file~~
−	~~# we are going to use the file mapping_info.txt to map Illumina IDs with patient IDs~~
−	~~# input will be~~
−
−	~~use Getopt::Long;~~
−	~~use Data::Dumper;~~
−	~~use strict;~~
−
−	~~my $VERSION = '1_00';~~
−
−	~~# Check if programm called correctly~~
−
−	~~my ($fp, $outdir, $fpout);~~
−	~~my $result = GetOptions ("infile=s" => \$fp,~~
−	~~"outfile=s"=> \$fpout,~~
−	~~"outdir=s"=> \$outdir);~~
−	~~if($fp eq "" \|\| $fpout eq "" \|\| $outdir eq "" ){~~
−	~~print "usage: perl extractPatients.pl -infile <csv file with SNP data> -outdir <output directory> -outfile <output file>\n";~~
−	~~exit(-1);~~
−	}
−
−	~~open(OUTPUT2, '>', $fpout) \|\| die("Could not open file $fpout!");~~
−	~~print2("#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");~~
−	~~print2("#Version: $VERSION\n");~~
−
−
−	~~#read in information about mapping between Illumina individuals and GSK individuals~~
−	~~# file has been created from "PGX40001_GSK_SJS_B137_29Aug2007_DNAReport.xls"~~
−
−	~~my $mapfp = 'mapping_info.txt';~~
−	~~open(DAT, $mapfp) \|\| die("Could not open file $mapfp!");~~
−	~~my @map_data=<DAT>;~~
−	~~my %map;~~
−	~~foreach my $m (@map_data) {~~
−	~~if ($m =~ !/^#/) {~~
−	~~$m =~ /(.)\t(.)\n/;~~
−	~~$map{lc $1} = $2~~
−	}
−	}
−	~~close(DAT);~~
−	~~if (!defined %map) {~~
−	~~print2("%map not defined");~~
−	~~die("%map not defined");~~
−	}
−	~~#print Dumper(\%map);~~
−
−	~~#$ head -30 PGx40001_12278-DNA.csv~~
−	~~#[Header]~~
−	~~#BSGT Version,3.1.10~~
−	~~#Processing Date,8/28/2007 11:53 AM~~
−	~~#Content,,Human1Mv1_C.bpm~~
−	~~#Num SNPs,1069083~~
−	~~#Total SNPs,1072820~~
−	~~#Num Samples,94~~
−	~~#Total Samples,292~~
−	~~#[Data]~~
−	~~#SNP Name,Sample ID,Allele1 - Forward,Allele2 - Forward,Allele1 - AB,Allele2 - AB,X,Y,X Raw,Y Raw,GC Score~~
−	~~#rs758676,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.420,0.611,3306,4684,0.8100~~
−	~~#rs3916934,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.341,0.511,2686,3914,0.9114~~
−	~~#rs2711935,WG0012278-DNA_A02_2949_A02,T,T,A,A,1.033,0.030,8298,255,0.9032~~
−	~~#rs17126880,WG0012278-DNA_A02_2949_A02,C,C,B,B,0.031,1.178,262,9201,0.9278~~
−	~~#rs12831433,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.947,1.015,7620,7947,0.8485~~
−	~~#rs12797197,WG0012278-DNA_A02_2949_A02,T,C,A,B,0.132,0.290,1062,2265,0.8524~~
−
−
−	~~open(DAT, $fp) \|\| die("Could not open file $fp!");~~
−
−	~~my $header=0;~~
−	~~my $l = 0;~~
−	~~my $oldId = "empty";~~
−
−	~~while (<DAT>) {~~
−	~~#ignore lines until we hit "[Data]"~~
−	~~#then read one more line~~
−	~~if ($header<2) {~~
−	~~if (/^\[Data\]/ \|\| $header >0) {~~
−	~~$header ++;~~
−	}
−	~~next;~~
−	}
−	~~$ l ++;~~
−	~~if (!($l % 100000)) {~~
−	~~print2 ("processing line $l\n");~~
−	}
−	~~my @line = split(/,/);~~
−
−	~~if (!defined $map{lc $line[1]}) {~~
−	~~print2( "unknown ID: " . $map{lc $line[1]} . ":::" . $line[1] . "\n");~~
−	}
−	~~if ($oldId ne $line[1]) {~~
−	~~if (<OUTFILE>) {~~
−	~~close (OUTFILE);~~
−	}
−	~~open(OUTFILE, ">", $outdir . "/" . $map{lc $line[1]} . ".txt");~~
−	~~print(OUTFILE "#perl extractPatients.pl -infile $fp -outdir $outdir -outfile $fpout\n");~~
−	~~print(OUTFILE "#Version: $VERSION\n");~~
−
−	}
−	~~$oldId = $line[1];~~
−
−	~~print (OUTFILE $line[0] . "\t" . $line[2] . "\t" . $line[3] . "\n");~~
−
−
−	~~#print "$_";~~
−	}
−	~~close(OUTFILE);~~
−	~~close(OUTPUT2);~~
−	~~#===============================~~
−
−	~~sub print2 {~~
−
−	~~my ($str) = @_;~~
−	~~print $str ;~~
−	~~print(OUTPUT2 $str);~~
−	}

ExtractPatients extractPatients - Revision history

Bjagla at 19:32, 18 October 2007

Bjagla at 19:07, 18 October 2007