[med-svn] [emmax] 04/10: Added example for the invocation of emmax once plink was run (or at least the ped file is available).

[Andreas Tille]

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tille pushed a commit to branch master
in repository emmax.

commit 7313df96c8d80bc14ea61d7bf4ac2e7cafb4acf8
Author: Steffen Moeller <moeller at debian.org>
Date:   Wed Jun 12 13:19:00 2013 +0000

    Added example for the invocation of emmax once
    plink was run (or at least the ped file is available).
---
 debian/emmax.examples        |  1 +
 debian/patches/logfile.patch | 24 ++++++++++++++++++++++++
 debian/patches/series        |  1 +
 debian/plink2emmax.sh        | 33 +++++++++++++++++++++++++++++++++
 4 files changed, 59 insertions(+)

diff --git a/debian/emmax.examples b/debian/emmax.examples
new file mode 100644
index 0000000..8204456
--- /dev/null
+++ b/debian/emmax.examples
@@ -0,0 +1 @@
+debian/plink2emmax.sh
diff --git a/debian/patches/logfile.patch b/debian/patches/logfile.patch
new file mode 100644
index 0000000..40fbdf3
--- /dev/null
+++ b/debian/patches/logfile.patch
@@ -0,0 +1,24 @@
+Index: emmax-0~beta.20100307/emmax.c
+===================================================================
+--- emmax-0~beta.20100307.orig/emmax.c
++++ emmax-0~beta.20100307/emmax.c
+@@ -1529,11 +1529,14 @@
+ 
+ void emmax_error( const char* format, ... ) {
+   va_list args;
+-  fprintf(g_logh.fp, "ERROR: ");
+-  va_start (args, format);
+-  vfprintf(g_logh.fp, format, args);
+-  va_end (args);
+-  fprintf(g_logh.fp,"\n");
++  if (g_logh.fp) {
++     // the logfile may not be available
++     fprintf(g_logh.fp, "ERROR: ");
++     va_start (args, format);
++     vfprintf(g_logh.fp, format, args);
++     va_end (args);
++     fprintf(g_logh.fp,"\n");
++  }
+ 
+   fprintf(stderr, "ERROR: ");
+   va_start (args, format);
diff --git a/debian/patches/series b/debian/patches/series
index 22b0179..f270a1f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ paths.patch
 aborts.patch
 install.patch
 clean.patch
+logfile.patch
diff --git a/debian/plink2emmax.sh b/debian/plink2emmax.sh
new file mode 100755
index 0000000..c372825
--- /dev/null
+++ b/debian/plink2emmax.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# Directly adapted from 
+# http://genome.sph.umich.edu/wiki/EMMAX
+
+set -e
+
+nosuffix=$1
+
+# preparing genomic input
+if [ ! -r $nosuffix.ped ]; then
+	if [ -r $nosuffix.bed ]; then
+		p-link --bfile $nosuffix --out --recode $nosuffix
+	else
+		echo "E: Could not find '$nosuffix.ped' or '$nosuffix.bed'."
+		exit -1
+	fi
+fi
+p-link --file $nosuffix --recode12 --output-missing-genotype 0 --transpose --out $nosuffix
+
+# Preparing phenotype input
+# Exchange -9 and 0 as phenotypes with NA
+awk '{print $1,$2,$6}' $nosuffix.ped > $nosuffix.emmax_phenotypes
+sed -i 's/-9$/NA/' $nosuffix.emmax_phenotypes
+sed -i 's/0$/NA/' $nosuffix.emmax_phenotypes
+
+# Creating Marker-Based Kinship Matrix
+emmax-kin -v -d 10 $nosuffix
+
+# Run EMMAX Association
+emmax -v -d 10 -t $nosuffix -p $nosuffix.emmax_phenotypes -k $nosuffix.BN.kinf -o $nosuffix.emmax
+
+echo "I: emmax completed successfully. Find results in '$nosuffix.emmax.ps'."

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