File size: 1,806 Bytes
9ae74ae | 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 | #!/bin/bash
if [ $# -eq 0 ]; then
echo >&2 ""
echo >&2 "silentextract by bcov - a tool to easily extract all tags from silent files"
echo >&2 "Usage:"
echo >&2 " silentextract myfile.silent"
echo >&2 "Flags:"
echo >&2 " -j cpus"
echo >&2 " -p param_file"
echo >&2 " @flags_file"
exit 1
fi
source $(dirname $(type -p "$0"))/_helpers/extract_flags.sh
silent=$1
extract_program=extract_pdbs
#https://stackoverflow.com/questions/592620/how-to-check-if-a-program-exists-from-a-bash-script/677212#677212
command -v extract_pdbs >/dev/null 2>&1 || {
#echo >&2 "You must have extract_pdbs on your path!";
#echo >&2 "Try doing cd silent_tools; ln -s /software/rosetta/latest/bin/extract_pdbs ."
#exit 1;
extract_program=pyextract_pdbs
}
#$extract_program -in:file:silent $silent -in:file:silent_struct_type binary -ignore_waters false -extra_res_fa /home/bcov/from/jason/H3i.am1bcc.fa.mm.params -extra_res_database_resname_list /home/nrbennet/software/silent_tools/extra_residues.list
if [ -z "${SILENT_J}" ]; then
# Do single-thread extraction
$extract_program -in:file:silent $silent -in:file:silent_struct_type binary $SILENT_PARAMS $SILENT_AT
else
# Do multi-thread extraction
tmp_fol=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13)
tmp_fol="tmp_${tmp_fol}"
rm -r $tmp_fol > /dev/null 2>&1
mkdir $tmp_fol
tmp_list="$tmp_fol/list"
cpus=${SILENT_J}
silentls $silent > $tmp_list
splitno=$((( $(wc -l $tmp_list | awk '{print $1}') / $cpus + 1)))
split -l $splitno $tmp_list $tmp_fol/x
ls $tmp_fol/x* | parallel -j$cpus "cat {} | silentslice $silent > {}.silent"
ls $tmp_fol/x*.silent | parallel -j$cpus 'silentextract {}'
rm $tmp_list
rm -r $tmp_fol
fi
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