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transl_to_mmcif_vrpt_from_pdbml_gz_worker.sh
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transl_to_mmcif_vrpt_from_pdbml_gz_worker.sh
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#!/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 < $FILE_LIST`
proc_id=0
while read pdbml_vrpt_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_vrpt_gz_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $pdbml_vrpt_gz_file -validation-full.xml.gz`
pdbml_vrpt_file=../${pdbml_vrpt_gz_file%.*} # remove the last '.gz'
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 $pdbml_vrpt_base ] && [ ! -e $WORK_DIR/$mmcif_vrpt_file ] && [ ! -e $div_dir/`basename $mmcif_vrpt_file`.gz ] ; then
touch $lock_file
( cd $WORK_DIR ; gunzip -c ../$pdbml_vrpt_gz_file > $pdbml_vrpt_base ; 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 ) || ( rm -f $pdbml_vrpt_base ; exit 1 ) )
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 < $FILE_LIST
proc_id=0
while read pdbml_vrpt_gz_file
do
proc_id_mod=$(($proc_id % $MAXPROCS))
if [ $proc_id_mod = $PROC_ID ] ; then
if [ ! -e $pdbml_vrpt_gz_file ] ; then
let proc_id++
continue
fi
pdb_id=`basename $pdbml_vrpt_gz_file -validation-full.xml.gz`
pdbml_vrpt_file=../${pdbml_vrpt_gz_file%.*} # remove the last '.gz'
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 $pdbml_vrpt_base ] && [ ! -e $WORK_DIR/$mmcif_vrpt_file ] && [ ! -e $div_dir/`basename $mmcif_vrpt_file`.gz ] ; then
touch $lock_file
( cd $WORK_DIR ; gunzip -c ../$pdbml_vrpt_gz_file > $pdbml_vrpt_base ; 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 ) || ( rm -f $pdbml_vrpt_base ; exit 1 ) )
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~