diff vcfs2fasta.sh @ 0:cb29f95c7b88 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfs2fasta.sh	Mon May 09 09:27:06 2016 -0400
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+echo $@
+
+OUTPUT=$1
+shift
+WITHMIXTURES=$1
+shift
+COLUMNNS=$1
+shift
+SAMPLENS=$1
+shift
+REFERENCE=$1
+shift
+INCLUDE=$1
+shift
+EXCLUDE=$1
+shift
+INPUT=$@
+
+CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT"
+
+if [ $WITHMIXTURES != "NOTTHERE" ]; then
+    CMD="$CMD --with-mixtures $WITHMIXTURES"
+fi
+
+if [ $COLUMNNS != "NOTTHERE" ]; then
+    CMD="$CMD --column-Ns $COLUMNNS"
+fi
+
+if [ $SAMPLENS != "NOTTHERE" ]; then
+    CMD="$CMD --sample-Ns $SAMPLENS"
+fi
+
+if [ $REFERENCE != "NOTTHERE" ]; then
+    CMD="$CMD --reference $REFERENCE"
+fi
+
+if [ $INCLUDE != "NOTTHERE" ]; then
+    CMD="$CMD --include INCLUDE"
+fi
+
+if [ $EXCLUDE != "NOTTHERE" ]; then
+    CMD="$CMD --exclude EXCLUDE"
+fi
+
+echo $CMD
+eval $CMD