/
gapseq
executable file
·84 lines (75 loc) · 2.99 KB
/
gapseq
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
#!/bin/bash
curdir=$(pwd)
path=$(readlink -f "$0")
dir=$(dirname "$path")
medium=$dir/dat/media/ALLmed.csv
usage()
{
echo "gapseq: prediction and analysis of bacterial metabolic pathways and genome-scale networks"
echo -e "\nUsage:"
echo " gapseq (find | find-transport | draft | fill | doall) (...)"
echo " gapseq doall (genome) [medium]"
echo " gapseq find (-p pathways | -e enzymes) [-b bitscore] (genome)"
echo " gapseq find-transport [-b bitscore] (genome)"
echo " gapseq draft (-r reactions | -t transporter -c genome -p pathways)"
echo " gapseq fill (-m draft -n medium -c rxn_weights -g rxn_genes)"
echo -e "\nExamples:"
echo " gapseq doall toy/ecoli.fna.gz"
echo " gapseq doall toy/myb71.fna.gz dat/media/TSBmed.csv"
echo " gapseq find -p chitin toy/myb71.fna.gz"
echo " gapseq find -p all toy/myb71.fna.gz"
echo " gapseq find-transport toy/myb71.fna.gz"
echo " gapseq draft -r toy/ecoli-all-Reactions.tbl -t toy/ecoli-Transporter.tbl -c toy/ecoli.fna.gz -p toy/ecoli-all-Pathways.tbl"
echo " gapseq fill -m toy/ecoli-draft.RDS -n dat/media/ALLmed.csv -c toy/ecoli-rxnWeights.RDS -g toy/ecoli-rxnXgenes.RDS"
echo -e "\nOptions:"
echo " find Pathway analysis, try to find enzymes based on homology."
echo " find-transport Search for transporters based on homology."
echo " draft Draft model construction based on results from find and find-transport."
echo " fill Gap filling of a model."
echo " doall Combine find, find-transport, draft and fill."
echo " -v Show version."
echo " -h Show this screen."
exit 1
}
OPTIND=1
while getopts ":h?vm:" opt; do
case "$opt" in
h|\?)
usage
exit 0
;;
v)
echo gapseq version: `git rev-parse --short HEAD`
exit 0
;;
esac
done
shift $((OPTIND-1))
[ "$1" = "--" ] && shift
[ "$#" -eq 0 ] && usage
if [ "$1" == "find" ]; then
parm=$(echo $@ | sed 's/find//')
$dir/src/gapseq_find.sh $parm
elif [ "$1" == "find-transport" ]; then
parm=$(echo $@ | sed 's/find-transport//')
$dir/src/transporter.sh $parm
elif [ "$1" == "draft" ]; then
parm=$(echo $@ | sed 's/draft//')
Rscript src/generate_GSdraft.R $parm
elif [ "$1" == "fill" ]; then
parm=$(echo $@ | sed 's/fill//')
Rscript $dir/src/gf.suite.R $parm
elif [ "$1" == "doall" ]; then
parm=$(echo $@ | sed 's/doall//')
file=$2
id="${file%.*}"
[[ ! -s "$file" ]] && usage
[[ $file == *.gz ]] && id="${id%.*}"
[[ -s "$3" ]] && medium=$3
$dir/src/gapseq_find.sh -v 0 -b 200 -p all -m bacteria $file
$dir/transporter.sh -b 200 $file
Rscript src/generate_GSdraft.R -r $id-all-Reactions.tbl -t $id-Transporter.tbl -c $file -u 200 -l 100 -a 1 -p $id-all-Pathways.tbl
Rscript src/gf.suite.R -m ./${id}.RDS -n $medium -c ./${id}-rxnWeights.RDS -b 100 -g ./${id}-rxnXgenes.RDS
else
usage
fi