-
Notifications
You must be signed in to change notification settings - Fork 1
/
transl_to_rdf_pdb_worker.sh
executable file
·174 lines (122 loc) · 4.22 KB
/
transl_to_rdf_pdb_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
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
#!/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 < $FILE_LIST`
proc_id=0
while read pdbml_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_gz_file ] ; then
let proc_id++
continue
fi
#pdb_id=`basename $pdbml_gz_file -noatom.xml.gz`
pdb_id=`basename $pdbml_gz_file -noatom-sifts.xml.gz`
rdf_file=$WORK_DIR/$pdb_id.rdf
div_dir=$WORK_DIR/${pdb_id:1:2}
err_file=$WORK_DIR/transl_to_rdf_pdb_$pdb_id.err
pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ ! -e $pdbml_file ] && ( ( [ ! -e $rdf_file ] && [ ! -e $div_dir/`basename $rdf_file`.gz ] ) || [ -e $err_file ] ) ; then
touch $lock_file
gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
#has_glycan=`java -jar $SAXON -s:$pdbml_file -xsl:$PDBML2WURCS_XSL`
#has_glycan=`xsltproc $PDBML2WURCS_XSL $pdbml_file`
#grep WURCS $pdbml_file > /dev/null
#has_glycan=$?
#if [ -z "$has_glycan" ] ; then
xsltproc -o $rdf_file --stringparam wurcs2glytoucan $WURCS_CATALOG_XML --stringparam primitive_type_mapping $_PDBX_PRIMITIVE_TYPE_MAPPING_XML $PDBML2RDF_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file || ( rm -f $pdbml_file $rdf_file ; cat $err_file ; exit 1 )
#else
# java -jar $SAXON -s:$pdbml_file -xsl:$PDBML2RDF_XSL -o:$rdf_file wurcs2glytoucan=$WURCS_CATALOG_XML primitive_type_mapping=$_PDBX_PRIMITIVE_TYPE_MAPPING_XML 2> $err_file && rm -f $err_file $pdbml_file || ( rm -f $pdbml_file $rdf_file ; cat $err_file ; exit 1 )
#fi
if [ $has_rapper_command != "false" ] && [ -s $rdf_file ] ; then
rapper -q -c $rdf_file 2> $err_file && rm -f $err_file || ( cat $err_file ; exit 1 )
fi
mk_div_dir $div_dir
if [ -s $rdf_file ] ; then
gzip_in_div_dir $rdf_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 < $FILE_LIST
proc_id=0
while read pdbml_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_gz_file ] ; then
let proc_id++
continue
fi
#pdb_id=`basename $pdbml_gz_file -noatom.xml.gz`
pdb_id=`basename $pdbml_gz_file -noatom-sifts.xml.gz`
rdf_file=$WORK_DIR/$pdb_id.rdf
div_dir=$WORK_DIR/${pdb_id:1:2}
err_file=$WORK_DIR/transl_to_rdf_pdb_$pdb_id.err
pdbml_file=${pdbml_gz_file%.*} # remove the last '.gz'
lock_file=$WORK_DIR/$pdb_id.lock
if [ ! -e $lock_file ] && [ ! -e $pdbml_file ] && [ ! -e $rdf_file ] && [ ! -e $div_dir/`basename $rdf_file`.gz ] ; then
touch $lock_file
gunzip -c $pdbml_gz_file > $pdbml_file || exit 1
#has_glycan=`java -jar $SAXON -s:$pdbml_file -xsl:$PDBML2WURCS_XSL`
#has_glycan=`xsltproc $PDBML2WURCS_XSL $pdbml_file`
#grep WURCS $pdbml_file > /dev/null
#has_glycan=$?
#if [ -z "$has_glycan" ] ; then
xsltproc -o $rdf_file --stringparam wurcs2glytoucan $WURCS_CATALOG_XML --stringparam primitive_type_mapping $_PDBX_PRIMITIVE_TYPE_MAPPING_XML $PDBML2RDF_XSL $pdbml_file 2> $err_file && rm -f $err_file $pdbml_file || ( rm -f $pdbml_file $rdf_file ; cat $err_file ; exit 1 )
#else
# java -jar $SAXON -s:$pdbml_file -xsl:$PDBML2RDF_XSL -o:$rdf_file wurcs2glytoucan=$WURCS_CATALOG_XML primitive_type_mapping=$_PDBX_PRIMITIVE_TYPE_MAPPING_XML 2> $err_file && rm -f $err_file $pdbml_file || ( rm -f $pdbml_file $rdf_file ; cat $err_file ; exit 1 )
#fi
if [ $has_rapper_command != "false" ] && [ -s $rdf_file ] ; then
rapper -q -c $rdf_file 2> $err_file && rm -f $err_file || ( cat $err_file ; exit 1 )
fi
mk_div_dir $div_dir
if [ -s $rdf_file ] ; then
gzip_in_div_dir $rdf_file $div_dir
fi
rm -f $lock_file
fi
fi
let proc_id++
done < $FILE_LIST~