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#!/usr/bin/env bash
if [ $# -ge 2 ]; then
tmpdir=$(mktemp -d -t relion_print_star_temp.XXXXXX)
# Get the desired data block
awk -v"tab=${2}" 'BEGIN {if (tab!~/^data_/) tab="data_"tab} (a==0 && $1==tab) {a=22; next} (a==22) {if ($1=="loop_") a+=1; else if ($1~/^data_/) exit;} (a==23) {if (length($0)<2 || $1~/^data_/) exit; else print $0;}' ${1} | grep -v loop_ > $tmpdir/tmp.dat
if [ $# == 2 ]; then # print all columns
awk '$1!~/^_/ {print;}' < $tmpdir/tmp.dat
else # print selected columns
awk '$1!~/^_/ {j++; print j}' < $tmpdir/tmp.dat > $tmpdir/tmp1.dat
for (( c=3; c<=$#; c++ )); do
awk -v"label=${!c}" 'BEGIN {if (label!~/^_/) label="_"label} {if ($1~/^_/) {i++; if ($1==label) col=i;} else {j++; print j, $col}}' < $tmpdir/tmp.dat > $tmpdir/tmp2.dat
join $tmpdir/tmp1.dat $tmpdir/tmp2.dat > $tmpdir/tmp3.dat
mv -f $tmpdir/tmp3.dat $tmpdir/tmp1.dat
done
awk '{for (i=2; i<=NF;i++) printf("%s%s", $i, (i==NF)?"\n":OFS)}' < $tmpdir/tmp1.dat
fi
rm -fr $tmpdir
else
echo " === Usage: === "
echo " ${0} <starfile> <tablename> [<label1> <label2> ...]"
echo " "
echo " === Purpose: === "
echo " This (bash) script prints the contents of a datablock (with name tablename) from a starfile"
echo " If any labels are given, then only those will be printed "
echo " "
echo " === Example: === "
echo " ${0} run3_it024_model.star data_model_class_1 rlnResolution rlnSsnrMap"
echo " (NOTE: not _rlnResolution)"
echo " "
echo " === Limitations: === "
echo " This program makes a temporary directory under \$TMPDIR. This folder must be writable and have sufficient space."
echo " "
echo " This program does not perform any error checks."
echo " When specified table and/or column(s) are absent in the input, the program might give incorrect results."
echo " In older versions, table names and column names could match only partially. For example, rlnFourierShellCorrelationCorrected matched rlnFourierShellCorrelation. This was dangerous and the match is exact now."
echo " "
echo " To address these issues, this program will be completely re-written in the next major update (RELION 3.2)."
echo " In the new version, the errors are handled more strictly. Please update your scripts to prepare for transition."
echo ""
fi
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