AnalysisPip2

#########################################################################
# File Name: test.sh
# Author: jdw
# mail: jiangdawei@icarbonx.com
# Created Time: Wed 24 Jan 2018 05:04:22 PM CST
#########################################################################
#!/bin/bash

if [ $# -lt 3 ]
then
        echo "Usage: $0 [Sample list] [Fastq Indir] [Outdir] "
        exit 1
fi

SampleList=$1
fqdir=$2
outdir=$3
mergedir=$outdir/merge
mkdir -p $outdir $mergedir

basepath=$(cd `dirname $0`;pwd)
MergeFq=$basepath/MergeFq
VsearchPip=$basepath/VsearchPip
plot=$basepath/plot.py
pcoa=$basepath/pcoa.py

echo "Start merge pair reads: "`date`
$MergeFq  $SampleList  $fqdir	$mergedir
echo "Start usearch analysis: "`date`
$VsearchPip  $mergedir/all.merged.fq  $outdir
echo "Start Result visualization: "`date`
$plot --path $outdir 
echo "Start PCoA analysis: "`date`
$pcoa --distance_file $outdir/beta/unifrac.txt --distance_type unifrac --outfile_prefix $outdir/beta/unifrac --group_file $SampleList --group_lable group