-
Notifications
You must be signed in to change notification settings - Fork 1
/
transl_to_mmcif_vrpt_worker.sh
executable file
·140 lines (94 loc) · 2.69 KB
/
transl_to_mmcif_vrpt_worker.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
126
127
128
129
130
131
132
133
134
135
136
137
138
139
#!/bin/bash
source ./scripts/env.sh
WORK_DIR=
FILE_LIST=
TOTAL=
ARGV=`getopt --long -o "d:l:n:t:" "$@"`
eval set -- "$ARGV"
while true ; do
case "$1" in
-d)
WORK_DIR=$2
shift
;;
-l)
FILE_LIST=$2
shift
;;
-n)
PROC_INFO=$2
shift
;;
-t)
TOTAL=$2
shift
;;
*)
break
;;
esac
shift
done
if ! [[ $PROC_INFO =~ .*of.* ]] ; then
echo "Invalid thread id ($PROC_INFO)."
exit 1
fi
MAXPROCS=`echo $PROC_INFO | cut -d 'f' -f 2`
PROC_ID=`echo $PROC_INFO | cut -d 'o' -f 1`
PROC_ID=$(($PROC_ID - 1))
# TOTAL=`wc -l < $FILE_LIST`
proc_id=0
while read pdbml_vrpt_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_vrpt_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $pdbml_vrpt_file -validation-full.xml`
pdbml_vrpt_base=`basename $pdbml_vrpt_file`
mmcif_vrpt_file=$pdb_id-validation-full.cif
div_dir=$WORK_DIR/${pdb_id:1:2}
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ ! -e $WORK_DIR/$mmcif_vrpt_file ] && [ ! -e $div_dir/`basename mmcif_vrpt_file`.gz ] ; then
touch $lock_file
( cd $WORK_DIR ; ln -s ../$pdbml_vrpt_file . ; xml2mmcif -xml $pdbml_vrpt_base -dict $pdbx_validation_dic -df $pdbx_validation_odb > /dev/null && rm -f $pdbml_vrpt_base && mv -f ../$pdbml_vrpt_base.cif $mmcif_vrpt_file && sed -i -e "s/\._\([0-9]\)\(\S*\) /\.\1\2 /" $mmcif_vrpt_file )
mk_div_dir $div_dir
if [ -s $WORK_DIR/$mmcif_vrpt_file ] ; then
gzip_in_div_dir $WORK_DIR/$mmcif_vrpt_file $div_dir
fi
rm -f $lock_file
fi
if [ $proc_id_mod -eq 0 ] ; then
echo -e -n "\rDone "$((proc_id + 1)) of $TOTAL ...
fi
fi
let proc_id++
done < $FILE_LIST
proc_id=0
while read pdbml_vrpt_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_vrpt_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $pdbml_vrpt_file -validation-full.xml`
pdbml_vrpt_base=`basename $pdbml_vrpt_file`
mmcif_vrpt_file=$pdb_id-validation-full.cif
div_dir=$WORK_DIR/${pdb_id:1:2}
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ ! -e $WORK_DIR/$mmcif_vrpt_file ] && [ ! -e $div_dir/`basename mmcif_vrpt_file`.gz ] ; then
touch $lock_file
( cd $WORK_DIR ; ln -s ../$pdbml_vrpt_file . ; xml2mmcif -xml $pdbml_vrpt_base -dict $pdbx_validation_dic -df $pdbx_validation_odb > /dev/null && rm -f $pdbml_vrpt_base && mv -f ../$pdbml_vrpt_base.cif $mmcif_vrpt_file && sed -i -e "s/\._\([0-9]\)\(\S*\) /\.\1\2 /" $mmcif_vrpt_file )
mk_div_dir $div_dir
if [ -s $WORK_DIR/$mmcif_vrpt_file ] ; then
gzip_in_div_dir $WORK_DIR/$mmcif_vrpt_file $div_dir
fi
rm -f $lock_file
fi
fi
let proc_id++
done < $FILE_LIST~