Newer
Older
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
#!/bin/bash
# gene-counts.sh
script_name="gene-counts.sh"
script_ver="1.0.0"
#Help function
usage() {
echo "-h Help documentation for $script_name"
echo "-a --Path to bam file"
echo "-b --Path to bam file2"
echo "-g --Path to the annotation file"
echo "-o --Path to output directory"
echo "-e --The experiment names."
echo "-v --Version of script"
echo "Example: $script_name -a 'foo_1.bam' -b 'foo_2.bam' -g '/path/to/gtf/gencode.v19.annotation.gtf' [-o '/path/to/output/dir/']"
exit 1
}
# Version function
version(){
echo "$script_name $script_ver"
exit 1
}
main(){
# Load required modules
module load RSEM/1.2.31
module load python/2.7.x-anaconda
module load picard/1.127
# Parsing options
OPTIND=1 # Reset OPTIND
while getopts :a:b:s:g:e:o:vh opt
do
case $opt in
a) aln_file_2=$OPTARG;;
b) aln_file_1=$OPTARG;;
g) transcriptome=$OPTARG;;
e) exp=$OPTARG;;
o) out=$OPTARG;;
v) version;;
h) usage;;
esac
done
shift $(($OPTIND -1))
# Check for mandatory options
if [[ -z $aln_file_1 ]] || [[ -z $aln_file_2 ]] || [[ -z $transcriptome ]] || [[ -z $exp ]]; then
usage
fi
# Define the output directory, if none defined make the location relative to first file
if [ -z $out ]; then
one_parent=$(dirname "${aln_file_1}")
out_dir=$(dirname "${one_parent}")\/$script_name-$script_ver/
else
out_dir=$out\/$script_name-$script_ver
fi
if [ ! -d $out_dir ]; then
mkdir $out_dir
fi
# If filtered alignment file doesn't exist
if [ ! -e $out_dir/$exp.counts ]; then
java -Xmx2g -jar $PICARD/picard.jar MergeSamFiles OUTPUT=$out_dir/$exp.bam INPUT=$aln_file_1 INPUT=$aln_file_2
rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 $out_dir/$exp.bam $transcriptome $out_dir/$output_fp
rm $out_dir/$exp.bam
# Get input and output files and then print out metadata.json file
input_files=("$aln_file_1", "$aln_file_2", "$transcriptome")
printf -v input "\"%s\"," "${input_files[@]}"
input=${input%,}
output_file=($out_dir/$output_fp*)
printf -v output "\"%s\"," "${output_file[@]}"
output=${output%,}
printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output" | python -m json.tool > $out_dir/$output_fp.metadata.json
else
echo "* Counts have already been called for $raw_fn"
fi
}
main "$@"