patch_rename

#!/bin/bash

scriptdir="$(dirname $(which $0))"

. ${scriptdir}/server.conf

: ${basedir:=$(pwd)}
: ${sampleset:=sampleset}
: ${working:=working}

cd ${basedir}


# Helper
fail() {
	printf '\e[31;1mArgh: %s\e[0m\n'	"$1"	1>&2
	[[ -n "$2" ]] && echo "$2" 1>&2
	exit 1
}

oops() {
	printf '\e[33;1mOops:%s\e[0m\n'	"$1"	 1>&2
}

title() {
	printf '\e[34;1m======================\n%s\n======================\e[0m\n\n'	"$1"
}

message() {
	printf '\e[37;1m%s\t%s\e[0m\n' "$1" "$2"
}

status() {
	printf '\e[36;1m%s\e[0m\n'	"$1"
}


# fetch batch description
if [[ -z "${1}" || "${1}" == "--help" ]]; then
	cat <<USAGE
Usage:
	$0 [ --patch <patchfile> ] <batchname>
Applies samplename patch after the fact.
USAGE
	exit
fi

# forced patchname ?
patchfile=
if [[  "${1}" == "--patch" ]]; then
	shift
	patchfile="${1}"
	shift
fi

# get batch
batchname="${1}"
byml="${sampleset}/batch.${batchname}.yaml"
[[ -r "${byml}" ]] || fail "Cannot open ${byml}"

# get patchname (if not provided)
if [[ -z "${patchfile}" ]]; then
	echo "autodetecting patchmap for ${batchname}"
	# parse batch description
	batch=$(<${byml})
	[[ "${batch}" =~ lab:[[:space:]]+([[:alnum:]]+) ]] || fail "Cannot find lab" $'file was:\n'"${batch}"
	lab="${BASH_REMATCH[1]}"
	case "$lab" in
		fgcz)
			echo "patch remapping for fgcz"
			if [[ "${2}" == "--force" ]]; then
				patchfile="${3}"
				echo "forcing patchfile ${patchfile}"
			else
				# TODO fallback to projects.{batch}.tsv
				[[ "${batch}" =~ order:[[:space:]]+o?([[:digit:]]+) ]] || fail "Cannot find order" $'file was:\n'"${batch}"
				order="${BASH_REMATCH[1]}"
				echo "order ${order}"
				[[ "${batch}" =~ project:[[:space:]]+p?([[:digit:]]+) ]] || fail "Cannot find project" $'file was:\n'"${batch}"
				project="${BASH_REMATCH[1]}"
				echo "project ${project}"
				patchfile="${sampleset}/patch.${project}.${order}.tsv"
			fi
		;;
		*)
			fail "Unknown lab $lab"
		;;
	esac
fi

# look for patchfile
[[ -r "${patchfile}" ]] || fail "Cannot open ${patchfile}"
echo "patchfile: ${patchfile}"

# patch samples in sampleset and working
declare -A map
while read old new trash; do
	map[$old]="${new}"

	if [[ -e "${working}/samples/${new}" ]]; then
		oops "$old -> $new already moved"
		continue
	fi

	longold="${old}-${batchname}"
	longnew="${new}-${batchname}"

	mkdir -p "${sampleset}/${new}"
	mv -v "${sampleset}/${old}/${batchname}" "${sampleset}/${new}/"
	touch --reference="${sampleset}/${old}" "${sampleset}/${new}"
	rmdir "${sampleset}/${old}"

	mkdir -p "${working}/samples/${new}"
	mv -v "${working}/samples/${old}/${batchname}" "${working}/samples/${new}/"
	
	mv "${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz"{,.old}
	zcat "${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz.old" | sed "1s/${longold}/${longnew}/g" | gzip >"${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz"
	touch --reference="${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz.old" "${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz"
	rm "${working}/samples/${new}/${batchname}/alignments/basecnt.tsv.gz.old"

	mv "${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz"{,.old}
	zcat "${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz.old" | sed "1s/${longold}/${longnew}/g" | gzip >"${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz"
	touch --reference="${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz.old" "${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz"
	rm "${working}/samples/${new}/${batchname}/alignments/coverage.tsv.gz.old"

	sed -si "1s/${longold}/${longnew}/g" "${working}/samples/${new}/${batchname}/alignments/REF_aln_stats.yaml" "${working}/samples/${new}/${batchname}/references/"*.fasta
	sed -i "s@${old}([-/])${batchname}@${new}\{1}${batchname}@g;s/^${longold:0:6}/${longnew:0:6}/g" "${working}/samples/${new}/${batchname}/references/"*.matcher
	sed -i "s/${longold}/${longnew}/g" "${working}/samples/${new}/${batchname}/references/frameshift_deletions_check.tsv"

	touch --reference="${working}/samples/${old}" "${working}/samples/${new}"
	rmdir "${working}/samples/${old}"
done < "${patchfile}"

# patch sample tsv list
mv "${sampleset}/samples.${batchname}.tsv"{,.old}
while read old batch len proto; do
	new="${old}"
	if [[ -z ${map[$old]} ]]; then
		oops "tsv $new not in patch list"
	else
		new="${map[$old]}"
	fi
	printf "%s\t%s\t%u\t%s\n" "${new}" "${batch}" "${len}" "${proto}"
done < "${sampleset}/samples.${batchname}.tsv.old" > "${sampleset}/samples.${batchname}.tsv"
#rm "${sampleset}/samples.${batchname}.tsv.old"

# patch projects tsv list
mv "${sampleset}/projects.${batchname}.tsv"{,.old}
while read old project order folder plate; do
	new="${old}"
	if [[ -z ${map[$old]} ]]; then
		oops "tsv $new not in patch list"
	else
		new="${map[$old]}"
	fi
	printf "%s\t%s\t%s\t%s\t%s\n" "${new}" "${project}" "${order}" "${folder}" "${plate}"
done < "${sampleset}/projects.${batchname}.tsv.old" > "${sampleset}/projects.${batchname}.tsv"
#rm "${sampleset}/projects.${batchname}.tsv.old"