-
Notifications
You must be signed in to change notification settings - Fork 0
/
scan_MINUS_strand_virus.sh
executable file
·126 lines (112 loc) · 4.31 KB
/
scan_MINUS_strand_virus.sh
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
# _____________________________________________________________________________
# -----------------------------------------------------------------------------
# Ensure we do not run the script with
# -----------------------------------------------------------------------------
# do not run the script if we try to use an uninitialized variable
##set -u
# exit the script, if any statement has a non-true return value
##set -e
# _____________________________________________________________________________
# -----------------------------------------------------------------------------
# Read in the parameters
# -----------------------------------------------------------------------------
usage()
{
cat << EOF
usage: $0 options
OPTIONS:
-c The directory that contains the scripts (GitRepo).
-v The path/name of the virtual environment (Conda).
-r The path to the results directory.
-t The site score threshold to be used.
-g The genome file to run on.
-n The name of the genome.
-h Print the script help.
EOF
}
if [ $# -lt 1 ] ; then
usage
exit 1
fi
# _____________________________________________________________________________
# -----------------------------------------------------------------------------
# Declare input variables (DEBUG MODE)
# -----------------------------------------------------------------------------
code_dir=""
virtual_env=""
results_dir=""
threshold=""
genome_file=""
genome_name=""
unset code_dir
unset virtual_env
unset results_dir
unset threshold
unset genome_file
unset genome_name
# -----------------------------------------------------------------------------
# Declare input variables (OPERATIVE MODE)
# -----------------------------------------------------------------------------
while getopts c:v:r:t:g:n:h: opt
do
case "$opt" in
c) code_dir=$OPTARG;;
v) virtual_env=$OPTARG;;
r) results_dir=$OPTARG;;
t) threshold=$OPTARG;;
g) genome_file=$OPTARG;;
n) genome_name=$OPTARG;;
h) usage;;
esac
done
# _____________________________________________________________________________
# -----------------------------------------------------------------------------
# check if we got an argument
if [ "$code_dir" == "" ] || [ "$virtual_env" == "" ] || [ "$results_dir" == "" ] || [ "$threshold" == "" ] || [ "$genome_file" == "" ] || [ "$genome_name" == "" ] ; then
usage
exit -1
fi
# _____________________________________________________________________________
# -----------------------------------------------------------------------------
# Give some feedback to the user on which files and directories are used
# -----------------------------------------------------------------------------
echo "________________________________________________________________________"
echo "------------------------------------------------------------------------"
echo "The directory with the code: ${code_dir}"
echo "The virtual environment used: ${virtual_env}"
echo "The directory to which the results will be written: ${results_dir}"
echo "The site prediction threshold used: ${threshold}"
echo "The genome file to be analysed: ${genome_file}"
echo "The genome name: ${genome_name}"
echo "------------------------------------------------------------------------"
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/beeond/software/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/beeond/software/miniconda3/etc/profile.d/conda.sh" ]; then
. "/beeond/software/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/beeond/software/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
# Load the conda environment
conda activate ${virtual_env}
# Run scan_fasta.py
python ${code_dir}/scan_fasta.py \
--genome_file ${genome_file} \
--pwm_file ${code_dir}/DATA/PWMs/attract_rbpdb_encode_filtered_human_pwms.h5 \
--out_home ${results_dir} \
--threshold ${threshold} \
--sense + \
--rcomp both \
--simN 1000 \
--simK 2 \
--out_tsv \
&> ${results_dir}/${genome_name}.log
conda deactivate
# Give some feedback so we know that the job finished successfully.
echo "Job finished successfully."