/usr/share/art-nextgen-simulation-tools/ART_profiler_illumina/art_profiler_illumina is in art-nextgen-simulation-tools-profiles 20160605+dfsg-2build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 | #!/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
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