File: art_profiler_illumina

package info (click to toggle)
art-nextgen-simulation-tools 20160605+dfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 15,948 kB
  • sloc: cpp: 7,952; perl: 524; sh: 210; makefile: 46
file content (177 lines) | stat: -rwxr-xr-x 6,015 bytes parent folder | download | duplicates (3)
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
177
#!/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