model/include/silent_tools/silentextract

#!/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