Differences

This shows you the differences between two versions of the page.

--- genetica:bonngwas_all [2013/01/31 13:10] – created tgif
+++ genetica:bonngwas_all [2020/08/04 10:58] (current) – external edit 127.0.0.1
@@ Line 48: / Line 48: @@
 my $ifile = shift;
 die "Must supply input filename!\n" unless ($ifile);
 (my $bn) = $ifile =~ /^(.*)\..*$/;
 my $pfile = $bn.'.proxies';
 my $ofile = $bn.'.pairs';
 my $tl = int qx/wc -l $ifile | awk {'print \$1'}/;
 open(IPF, "<$ifile") or die "Cant open input file\n";
 my @pairs;
 print "looking for pairs in $tl inputs...\n";
 my $l = 0;
 while(<IPF>){
 	(my $a, my $b) = /(rs\d{1,18})\s+(rs\d{1,18})/;
@@ Line 76: / Line 66: @@
 		my @aps = uniq get_proxies($a, $pfile);
 		my @bps = uniq get_proxies($b, $pfile);
 		foreach my $ap (sort @aps){
 			foreach my $bp (sort @bps){
@@ Line 119: / Line 108: @@
 }
 </code>
+.- Tras esto ya se puede correr intersnp deuna manera racional.
+Para los dos ultimos pasos hemos hecho un script que engloba el procesamiento de un test en todas las DBs.
+<code perl isnp4all.pl>
+use strict; use warnings;
+use File::Basename qw(basename);
+use File::Find::Rule;
+my $origpairs = shift;
+my @dbs = qw(ADMURimpQC2 ADNIimpQC2 GenADA_impQC2 NIA_AD_impQC2 TGEN_impQC2);
+my $sel_template = '/home/data/Bonn_GWAS/selection_file_template.txt';
+(my $test) = $origpairs =~ /listTEST(\d*)\.pairs/;
+my $w_dir = 'intersnp_TEST'.$test;
+mkdir $w_dir;
+chdir $w_dir;
+my $odir = 'outputs';
+mkdir $odir;
+my $tmpsel = 'selection_file_TEST'.$test.'.txt';
+foreach my $dbname (@dbs){
+	my $targetdb = '/home/data/Variomics/'.$dbname;
+	my $grpfile = 'listTEST'.$test.'_'.$dbname.'.grp';
+	my $order ='grppairs.pl '.$origpairs.' '.$targetdb.'.bim > '.$grpfile;
+	print "Grep $origpairs into $dbname...\n";
+	system($order);
+	print "Done\n";
+	open TEMPLATE, "<$sel_template" or die "Could not find template\n";
+	open TMPS, ">$tmpsel";
+	my $ofile = $odir.'/'.$dbname.'_TEST'.$test.'_';
+	while (<TEMPLATE>){
+		s/<Database>/$targetdb/;
+		s/<Test>/$test/;
+		s/<Pairs>/$grpfile/;
+		s/<Output>/$ofile/;
+		print TMPS "$_";
+	}
+	close TMPS;
+	close TEMPLATE;
+#	my $order = 'intersnpPN '.$tmpsel;
+#	system($order);
+	$order = 'intersnp '.$tmpsel;
+	print "$order\n";
+	system($order);
+}
+</code>
+Para ello utilizamos la plantilla,
+<code>
+$ cat selection_file_template.txt
+BFILE   <Database>  // put path and name of plink bfile there
+TWO_MARKER 1
+PRINTTOP 50000
+TEST <Test>
+COMBIFILE <Pairs>  // if file is in working dir, else put path
+COMBILIST 1
+OUTPUTNAME <Output>
+END
+</code>