art-nextgen-simulation-tools 20160605+dfsg-2build1 / usr / bin / art_profiler_illumina

#!/bin/bash
# Description: this script is to create Illumina read profile from multiple fastq or gzipped fastq files
# Author: Weichun Huang at <whduke@gmail.com>
# Lastest update on Fri Apr 15 16:34:45 EDT 2016
# License: GPL v3
#---------------------------------------------------------------------------
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
#---------------------------------------------------------------------------

ext=fq
nthreads=1
if [[ $# -eq 3 ]];then
       	outFile=$1
	iDIR=$2
	ext=$3
       	if type nproc 2>/dev/null 1>&2; then
	       	nthreads=`nproc`
       	elif type sysctl 2>/dev/null 1>&2; then  
		nthreads=`sysctl -n hw.ncpu`
       	else
	       	echo "warning: use only one threads as the program failed to detect #cores in the system" 
		nthreads=1
       	fi
elif [[ $# -eq 4 ]];then
       	outFile=$1
	iDIR=$2
	ext=$3
       	nthreads=$4
        re='^[0-9]+$'
	if ! [[ $nthreads =~ $re ]] || (($nthreads <= 0)); then
	       	echo "Error: number of cores must be a positive integer " >&2; exit 1
       	fi
else
        echo "This tool is to create an Illumina read quality profile from multiple fastq or gzipped fastq files"
	echo ""
	echo "USAGE:"
	echo "	./art_profiler_illumina output_profile_name input_fastq_dir fastq_filename_extension [max_number_threads]"
	echo ""
	echo "PARAMETERS:"
       	echo "	output_profile_name:  the name of read quality profile to be generated"  
       	echo "	input_fastq_dir:   the directory of input fastq or zipped fastq files"  
       	echo "	fastq_filename_extension: fastq or gzipped fastq filename extension"
       	echo "	max_number_threads:: maximum number of threads/cores to be used for the run (default: all cores)"
	echo ""
	echo "EXAMPLES:"
	echo "	1) create hiseq2k profiles from all *.fq.gz in the directory fastq_dat_dir"
	echo "		./art_profiler_illumina hiseq2k fastq_dat_dir fq.gz"
	echo "	2) create miseq2500 profiles from all *.fq in the directory fastq_dat_dir"
	echo "		./art_profiler_illumina miseq250 fastq_dat_dir fq"
	echo "	3) create hiseq1k profiles from all *.fq in the directory fastq_dat_dir using 20 threads"
	echo "		./art_profiler_illumina hiseq1k fastq_dat_dir fq 20"
       	echo ""       
	echo "NOTES: For paired-end fastq files, e.g., *.fq or *.fq.gz,"
       	echo "       the filenames of the 1st reads must be *_1.fq/*_1.fq.gz, or *.1.fq/*.1.fq.gz"
       	echo "       and those of the 2nd reads must be *_2.fq./*_2.fq.gz, or *.2.fq or *.2.fq.gz"
       	echo ""       
	echo "CONTACT: Weichun Huang at whduke@gmail.com"
	exit 1
fi

if  [[ ! -e $iDIR ]]; then echo "Error: directory $iDIR does not exist"; exit 1; fi
ls $iDIR/*.$ext 2>/dev/null 1>&2
if [ $? -gt 0 ]; then echo "Error: no *.$ext fastq files in $iDIR"; exit 1;  fi

pDIR=/usr/lib/art-nextgen-simulation-tools
export pDIR
export ext;

oList=
of1st=
of2nd=
i=0
k1=0
k2=0
for fq in $iDIR/*.$ext 
do
# using xargs instead
#       	$pDIR/fastqReadAvg.pl $fq & 
        t1=${fq%_1.$ext}	
        t1=${t1%.1.$ext}	
        t2=${fq%_2.$ext}	
        t2=${t2%.2.$ext}	

	if [[ $t1 != $fq ]];then 
		of1st="$of1st ${fq#$iDIR\/}.txt"
	       	k1=$((k1+1))
	elif [[ $t2 != $fq ]];then 
		of2nd="$of2nd ${fq#$iDIR\/}.txt"
	       	k2=$((k2+1))
	else
	       	oList="$oList ${fq#$iDIR\/}.txt"
	       	i=$((i+1))
	fi
done

#thanks Lee Katz at <lkatz@cdc.gov> for suggesting using xargs
ls -S $iDIR/*.$ext | xargs -P $nthreads -n 1 bash -c '
  b=$(basename $0 .$ext);
  if [ -e $b.$ext.txt ]; then
	  echo "already processed the file $0"
	  echo "remove $b.$ext.txt to re-process $0"
	  exit 0;
  fi
  echo "processing $0"
  $pDIR/fastqReadAvg.pl $0
  if [ $? -gt 0 ]; then echo "Error in running fastqReadAvg.pl on $0"; exit 1; fi;
'
if [ $? -gt 0 ]; then 
  echo "Error in processing at least one or more fastq files" 
  exit 1 
fi

if [[ $i -ge 1 ]]; then
       	if [[ $i -eq 1 ]]; then
	       	mv $oList $outFile.freq.txt
       	else 
		$pDIR/summation.pl $oList $outFile.freq.txt
		if [ $? -gt 0 ]; then exit 1; fi
       	fi
       	$pDIR/combinedAvg.pl $outFile.freq.txt
	if [ $? -gt 0 ]; then exit 1; fi;
       	$pDIR/empDist.pl $outFile.freq.txt $outFile.txt
       	if [[ $? == 0 ]]; then
	       	echo "The read profile file $outFile.txt has been created"
	else 
		exit 1 
       	fi
       	rm -fr $oList $outFile.freq.txt
fi	

if [[ $k1 -ge 1 ]]; then
       	if [[ $k1 -eq 1 ]]; then
	       	mv $of1st ${outFile}R1.freq.txt
       	else 
		$pDIR/summation.pl $of1st ${outFile}R1.freq.txt
	if [ $? -gt 0 ]; then exit 1; fi;
       	fi
       	$pDIR/combinedAvg.pl ${outFile}R1.freq.txt
	if [ $? -gt 0 ]; then exit 1; fi;
       	$pDIR/empDist.pl ${outFile}R1.freq.txt ${outFile}R1.txt
       	if [[ $? == 0 ]]; then
	       	echo "The read profile file ${outFile}R1.txt has been created"
	else 
		exit 1; 
       	fi
       	rm -fr $of1st ${outFile}R1.freq.txt
fi

if [[ $k2 -ge 1 ]]; then
       	if [[ $k2 -eq 1 ]]; then
	       	mv $of2nd ${outFile}R2.freq.txt
       	else 
		$pDIR/summation.pl $of2nd ${outFile}R2.freq.txt
		if [ $? -gt 0 ]; then exit 1; fi;
       	fi
       	$pDIR/combinedAvg.pl ${outFile}R2.freq.txt
	if [ $? -gt 0 ]; then exit 1; fi;
       	$pDIR/empDist.pl ${outFile}R2.freq.txt ${outFile}R2.txt
       	if [[ $? == 0 ]]; then
	       	echo "The read profile file ${outFile}R2.txt has been created"
	else 
		exit 1; 
       	fi
       	rm -fr $of2nd ${outFile}R2.freq.txt
fi