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databases.sh
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databases.sh
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#!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
hasCommand () {
command -v "$1" >/dev/null 2>&1
}
ARR=""
push_back() {
# shellcheck disable=SC1003
CURR="$(printf '%s' "$1" | awk '{ gsub(/'\''/, "'\''\\'\'''\''"); print; }')"
if [ -z "$ARR" ]; then
ARR=''\'$CURR\'''
else
ARR=$ARR' '\'$CURR\'''
fi
}
STRATEGY=""
if hasCommand aria2c; then STRATEGY="$STRATEGY ARIA"; fi
if hasCommand curl; then STRATEGY="$STRATEGY CURL"; fi
if hasCommand wget; then STRATEGY="$STRATEGY WGET"; fi
if [ "$STRATEGY" = "" ]; then
fail "No download tool found in PATH. Please install aria2c, curl or wget."
fi
downloadFile() {
URL="$1"
OUTPUT="$2"
set +e
for i in $STRATEGY; do
case "$i" in
ARIA)
FILENAME=$(basename "${OUTPUT}")
DIR=$(dirname "${OUTPUT}")
if aria2c -c --max-connection-per-server="$ARIA_NUM_CONN" --allow-overwrite=true -o "${FILENAME}.aria2" -d "$DIR" "$URL"; then
mv -f -- "${OUTPUT}.aria2" "${OUTPUT}"
return 0
fi
;;
CURL)
if curl -L -C - -o "${OUTPUT}.curl" "$URL"; then
mv -f -- "${OUTPUT}.curl" "${OUTPUT}"
return 0
fi
;;
WGET)
if wget -O "${OUTPUT}.wget" -c "$URL"; then
mv -f -- "${OUTPUT}.wget" "${OUTPUT}"
return 0
fi
;;
esac
done
set -e
fail "Could not download $URL to $OUTPUT"
}
# check number of input variables
[ "$#" -ne 3 ] && echo "Please provide <selection> <outDB> <tmp>" && exit 1;
[ ! -d "$3" ] && echo "tmp directory $3 not found!" && mkdir -p "$3";
SELECTION="$1"
OUTDB="$2"
TMP_PATH="$3"
INPUT_TYPE=""
case "${SELECTION}" in
"UniRef100")
if notExists "${TMP_PATH}/uniref100.fasta.gz"; then
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.release_note" "${TMP_PATH}/version"
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz" "${TMP_PATH}/uniref100.fasta.gz"
fi
push_back "${TMP_PATH}/uniref100.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"UniRef90")
if notExists "${TMP_PATH}/uniref90.fasta.gz"; then
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.release_note" "${TMP_PATH}/version"
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz" "${TMP_PATH}/uniref90.fasta.gz"
fi
push_back "${TMP_PATH}/uniref90.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"UniRef50")
if notExists "${TMP_PATH}/uniref50.fasta.gz"; then
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.release_note" "${TMP_PATH}/version"
downloadFile "https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz" "${TMP_PATH}/uniref50.fasta.gz"
fi
push_back "${TMP_PATH}/uniref50.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"UniProtKB")
if notExists "${TMP_PATH}/uniprot_sprot.fasta.gz" || notExists "${TMP_PATH}/uniprot_trembl.fasta.gz"; then
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/reldate.txt" "${TMP_PATH}/version"
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz" "${TMP_PATH}/uniprot_sprot.fasta.gz"
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz" "${TMP_PATH}/uniprot_trembl.fasta.gz"
fi
push_back "${TMP_PATH}/uniprot_sprot.fasta.gz"
push_back "${TMP_PATH}/uniprot_trembl.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"UniProtKB/TrEMBL")
if notExists "${TMP_PATH}/uniprot_trembl.fasta.gz"; then
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/reldate.txt" "${TMP_PATH}/version"
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz" "${TMP_PATH}/uniprot_trembl.fasta.gz"
fi
push_back "${TMP_PATH}/uniprot_trembl.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"UniProtKB/Swiss-Prot")
if notExists "${TMP_PATH}/uniprot_sprot.fasta.gz"; then
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/reldate.txt" "${TMP_PATH}/version"
downloadFile "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz" "${TMP_PATH}/uniprot_sprot.fasta.gz"
fi
push_back "${TMP_PATH}/uniprot_sprot.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"NR")
if notExists "${TMP_PATH}/nr.gz"; then
date "+%s" > "${TMP_PATH}/version"
downloadFile "https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz" "${TMP_PATH}/nr.gz"
downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz" "${TMP_PATH}/prot.accession2taxid.gz"
gunzip "${TMP_PATH}/prot.accession2taxid.gz"
downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pdb.accession2taxid.gz" "${TMP_PATH}/pdb.accession2taxid.gz"
gunzip "${TMP_PATH}/pdb.accession2taxid.gz"
fi
push_back "${TMP_PATH}/nr.gz"
INPUT_TYPE="FASTA_LIST"
;;
"NT")
if notExists "${TMP_PATH}/nt.gz"; then
date "+%s" > "${TMP_PATH}/version"
downloadFile "https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz" "${TMP_PATH}/nt.gz"
fi
push_back "${TMP_PATH}/nt.gz"
INPUT_TYPE="FASTA_LIST"
;;
"GTDB")
if notExists "${TMP_PATH}/download.done"; then
downloadFile "https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/VERSION.txt" "${TMP_PATH}/version"
downloadFile "https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/genomic_files_reps/gtdb_proteins_aa_reps.tar.gz" "${TMP_PATH}/gtdb.tar.gz"
downloadFile "https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_taxonomy.tsv" "${TMP_PATH}/bac120_taxonomy.tsv"
downloadFile "https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar53_taxonomy.tsv" "${TMP_PATH}/ar53_taxonomy.tsv"
touch "${TMP_PATH}/download.done"
fi
INPUT_TYPE="GTDB"
;;
"PDB")
if notExists "${TMP_PATH}/pdb_seqres.txt.gz"; then
date "+%s" > "${TMP_PATH}/version"
downloadFile "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz" "${TMP_PATH}/pdb_seqres.txt.gz"
fi
push_back "${TMP_PATH}/pdb_seqres.txt.gz"
INPUT_TYPE="FASTA_LIST"
;;
"PDB70")
if notExists "${TMP_PATH}/msa.index"; then
date "+%s" > "${TMP_PATH}/version"
downloadFile "http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_latest.tar.gz" "${TMP_PATH}/pdb70.tar.gz"
tar -xOzf "${TMP_PATH}/pdb70.tar.gz" pdb70_a3m.ffdata | tr -d '\000' | awk -v outfile="${TMP_PATH}/msa" 'function writeEntry() { printf "%s\0", data >> outfile; size = length(data) + 1; data=""; print id"\t"offset"\t"size >> outindex; offset = offset + size; } BEGIN { data = ""; offset = 0; id = 1; if(length(outfile) == 0) { outfile="output"; } outindex = outfile".index"; printf("") > outfile; printf("") > outindex; printf("%c%c%c%c",11,0,0,0) > outfile".dbtype"; } /^>ss_/ { inss = 1; entry = 0; next; } inss == 1 { inss = 0; next; } /^>/ && entry == 0 { if (id > 1) { writeEntry(); } id = id + 1; data = ">"substr($1, 2)"\n"; entry = entry + 1; next; } entry > 0 { data = data""$0"\n"; entry = entry + 1; next; } END { writeEntry(); close(outfile); close(outfile".index"); }'
rm -f "${TMP_PATH}/pdb70.tar.gz"
fi
INPUT_TYPE="A3M"
;;
"Pfam-A.full")
if notExists "${TMP_PATH}/db.msa.gz"; then
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz" "${TMP_PATH}/version"
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz" "${TMP_PATH}/db.msa.gz"
fi
INPUT_TYPE="STOCKHOLM_MSA"
;;
"Pfam-A.seed")
if notExists "${TMP_PATH}/db.msa.gz"; then
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz" "${TMP_PATH}/version"
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz" "${TMP_PATH}/db.msa.gz"
fi
INPUT_TYPE="STOCKHOLM_MSA"
;;
"Pfam-B")
if notExists "${TMP_PATH}/msa.tar.gz"; then
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz" "${TMP_PATH}/version"
downloadFile "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-B.tgz" "${TMP_PATH}/msa.tar.gz"
fi
INPUT_TYPE="FASTA_MSA"
;;
"eggNOG")
if notExists "${TMP_PATH}/download.done"; then
date "+%s" > "${TMP_PATH}/version"
downloadFile "http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/2/2_raw_algs.tar" "${TMP_PATH}/bacteria.tar"
downloadFile "http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/2157/2157_raw_algs.tar" "${TMP_PATH}/archea.tar"
downloadFile "http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/2759/2759_raw_algs.tar" "${TMP_PATH}/eukaryota.tar"
downloadFile "http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/10239/10239_raw_algs.tar" "${TMP_PATH}/viruses.tar"
touch "${TMP_PATH}/download.done"
fi
INPUT_TYPE="eggNOG"
push_back "${TMP_PATH}/bacteria.tar"
push_back "${TMP_PATH}/archea.tar"
push_back "${TMP_PATH}/eukaryota.tar"
push_back "${TMP_PATH}/viruses.tar"
TAR2DB_INCLUDE='\.raw_alg\.faa\.gz$'
SED_FIX_LOOKUP='s|\.raw_alg\.faa\.gz||g'
;;
"VOGDB")
if notExists "${TMP_PATH}/download.done"; then
downloadFile "http://fileshare.csb.univie.ac.at/vog/latest/release.txt" "${TMP_PATH}/version"
downloadFile "http://fileshare.csb.univie.ac.at/vog/latest/vog.raw_algs.tar.gz" "${TMP_PATH}/vog.tar.gz"
touch "${TMP_PATH}/download.done"
fi
INPUT_TYPE="eggNOG"
push_back "${TMP_PATH}/vog.tar.gz"
TAR2DB_INCLUDE='\.msa$'
SED_FIX_LOOKUP='s|\.msa||g'
;;
"CDD")
if notExists "${TMP_PATH}/msa.msa.gz"; then
downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/cdd.info" "${TMP_PATH}/version"
downloadFile "https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/fasta.tar.gz" "${TMP_PATH}/msa.tar.gz"
fi
INPUT_TYPE="FASTA_MSA"
SED_FIX_LOOKUP='s|\.FASTA||g'
FASTA_MSA_MSA2PROFILE_PAR="--skip-query"
;;
"Resfinder")
if notExists "${TMP_PATH}/download.done"; then
downloadFile "https://api.bitbucket.org/2.0/repositories/genomicepidemiology/resfinder_db/commit/master?fields=hash,date" "${TMP_PATH}/version"
downloadFile "https://bitbucket.org/genomicepidemiology/resfinder_db/get/master.tar.gz" "${TMP_PATH}/master.tar.gz"
# avoid tar wildcard extraction as it's not available in busybox tar (windows, biocontainer)
mkdir -p "${TMP_PATH}/fsa"
tar -C "${TMP_PATH}/fsa" --strip-components=1 -xzvf "${TMP_PATH}/master.tar.gz"
mv -f -- "${TMP_PATH}/fsa/"*.fsa "${TMP_PATH}"
rm -rf -- "${TMP_PATH}/master.tar.gz" "${TMP_PATH}/fsa"
touch "${TMP_PATH}/download.done"
fi
INPUT_TYPE="FSA"
;;
"dbCAN2")
if notExists "${TMP_PATH}/download.done"; then
downloadFile "http://bcb.unl.edu/dbCAN2/download/dbCAN-fam-aln-V9.tar.gz" "${TMP_PATH}/msa.tar.gz"
printf "9 %s\n" "$(date "+%s")" > "${TMP_PATH}/version"
touch "${TMP_PATH}/download.done"
fi
INPUT_TYPE="FASTA_MSA"
SED_FIX_LOOKUP='s|\.aln||g'
;;
"SILVA")
if notExists "${TMP_PATH}/download.done"; then
downloadFile "https://ftp.arb-silva.de/release_${SILVA_REL}/Exports/README.txt" "${TMP_PATH}/version"
downloadFile "https://ftp.arb-silva.de/release_${SILVA_REL}/Exports/SILVA_${SILVA_REL}_SSURef_NR99_tax_silva.fasta.gz" "${TMP_PATH}/silva.fasta.gz"
downloadFile "https://ftp.arb-silva.de/release_${SILVA_REL}/Exports/taxonomy/tax_slv_ssu_${SILVA_REL}.txt.gz" "${TMP_PATH}/silva_tax.txt.gz"
gunzip "${TMP_PATH}/silva_tax.txt.gz"
downloadFile "https://ftp.arb-silva.de/release_${SILVA_REL}/Exports/taxonomy/tax_slv_ssu_${SILVA_REL}.acc_taxid.gz" "${TMP_PATH}/silva.acc_taxid.gz"
gunzip "${TMP_PATH}/silva.acc_taxid.gz"
touch "${TMP_PATH}/download.done"
fi
push_back "${TMP_PATH}/silva.fasta.gz"
INPUT_TYPE="FASTA_LIST"
;;
"Kalamari")
if notExists "${TMP_PATH}/kalamari.tsv"; then
printf "3.7 %s\n" "$(date "+%s")" > "${TMP_PATH}/version"
downloadFile "https://raw.githubusercontent.com/lskatz/Kalamari/18d71da740546ba4a5117682e1ae2a037379afe0/src/Kalamari_v3.7.tsv" "${TMP_PATH}/kalamari.tsv"
fi
ACCESSIONS=""
# shellcheck disable=SC2034
while IFS="$(printf '\t')" read -r NAME ACCESSION TAXID; do
if [ "$NAME" = "scientificName" ]; then
continue
fi
case "${ACCESSION}" in XXX*)
continue
esac
if [ -z "$ACCESSIONS" ]; then
ACCESSIONS="$ACCESSION"
else
ACCESSIONS="$ACCESSIONS,$ACCESSION"
fi
done < "${TMP_PATH}/kalamari.tsv"
if notExists "${TMP_PATH}/kalamari.fasta"; then
# Reset download strategy to not use aria2c for NCBI
STRATEGY=""
if hasCommand curl; then STRATEGY="$STRATEGY CURL"; fi
if hasCommand wget; then STRATEGY="$STRATEGY WGET"; fi
if [ "$STRATEGY" = "" ]; then
fail "No download tool found in PATH. Please install aria2c, curl or wget."
fi
downloadFile "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${ACCESSIONS}&rettype=fasta&retmode=txt" "${TMP_PATH}/kalamari.fasta.tmp"
awk '/<!DOCTYPE/ { exit 1; } ' "${TMP_PATH}/kalamari.fasta.tmp" || fail "Could not download genomes from NCBI. Please try again later."
awk -F '[\t>.]' 'NR == FNR { f[$2]=$NF; next; } /^>/{ print $0" TaxID="f[$2]" "; next; } { print; }' "${TMP_PATH}/kalamari.tsv" "${TMP_PATH}/kalamari.fasta.tmp" > "${TMP_PATH}/kalamari.fasta"
rm -f "${TMP_PATH}/kalamari.fasta.tmp"
fi
push_back "${TMP_PATH}/kalamari.fasta"
INPUT_TYPE="FASTA_LIST"
;;
esac
if notExists "${OUTDB}.dbtype"; then
case "${INPUT_TYPE}" in
"FASTA_LIST")
eval "set -- $ARR"
# shellcheck disable=SC2086
"${MMSEQS}" createdb "${@}" "${OUTDB}" ${COMP_PAR} \
|| fail "createdb died"
for i in "${@}"; do
rm -f -- "$i"
done
;;
"FSA")
# shellcheck disable=SC2086
"${MMSEQS}" createdb "${TMP_PATH}/"*.fsa "${OUTDB}" ${COMP_PAR} \
|| fail "createdb died"
rm -f -- "${TMP_PATH}/"*.fsa
;;
"A3M")
# shellcheck disable=SC2086
"${MMSEQS}" msa2profile "${TMP_PATH}/msa" "${OUTDB}" --match-mode 1 --match-ratio 0.5 --msa-type 1 ${THREADS_PAR} \
|| fail "msa2profile died"
;;
"STOCKHOLM_MSA")
# shellcheck disable=SC2086
"${MMSEQS}" convertmsa "${TMP_PATH}/db.msa.gz" "${TMP_PATH}/msa" ${VERB_PAR} \
|| fail "convertmsa died"
rm -f "${TMP_PATH}/db.msa.gz"
# shellcheck disable=SC2086
"${MMSEQS}" msa2profile "${TMP_PATH}/msa" "${OUTDB}" --match-mode 1 --match-ratio 0.5 ${THREADS_PAR} \
|| fail "msa2profile died"
if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"${MMSEQS}" rmdb "${TMP_PATH}/msa" ${VERB_PAR} \
|| fail "rmdb died"
fi
;;
"FASTA_MSA")
# shellcheck disable=SC2086
"${MMSEQS}" tar2db "${TMP_PATH}/msa.tar.gz" "${TMP_PATH}/msa" --output-dbtype 11 ${THREADS_PAR} \
|| fail "tar2db died"
if [ -n "${SED_FIX_LOOKUP}" ]; then
sed "${SED_FIX_LOOKUP}" "${TMP_PATH}/msa.lookup" > "${TMP_PATH}/msa.lookup_tmp"
mv -f -- "${TMP_PATH}/msa.lookup_tmp" "${TMP_PATH}/msa.lookup"
fi
rm -f -- "${TMP_PATH}/msa.tar.gz"
# shellcheck disable=SC2086
"${MMSEQS}" msa2profile "${TMP_PATH}/msa" "${OUTDB}" --match-mode 1 --match-ratio 0.5 ${FASTA_MSA_MSA2PROFILE_PAR} ${THREADS_PAR} \
|| fail "msa2profile died"
if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"${MMSEQS}" rmdb "${TMP_PATH}/msa" ${VERB_PAR} \
|| fail "rmdb died"
fi
;;
"eggNOG")
eval "set -- $ARR"
# shellcheck disable=SC2086
"${MMSEQS}" tar2db "${@}" "${TMP_PATH}/msa" --output-dbtype 11 --tar-include "${TAR2DB_INCLUDE}" ${THREADS_PAR} \
|| fail "tar2db died"
rm -f -- "${@}"
if [ -n "${SED_FIX_LOOKUP}" ]; then
sed "${SED_FIX_LOOKUP}" "${TMP_PATH}/msa.lookup" > "${TMP_PATH}/msa.lookup_tmp"
mv -f -- "${TMP_PATH}/msa.lookup_tmp" "${TMP_PATH}/msa.lookup"
fi
sed 's|\.raw_alg\.faa\.gz||g' "${TMP_PATH}/msa.lookup" > "${TMP_PATH}/msa.lookup.tmp"
mv -f -- "${TMP_PATH}/msa.lookup.tmp" "${TMP_PATH}/msa.lookup"
# shellcheck disable=SC2086
"${MMSEQS}" msa2profile "${TMP_PATH}/msa" "${OUTDB}" --match-mode 1 --match-ratio 0.5 ${THREADS_PAR} \
|| fail "msa2profile died"
mv -f -- "${TMP_PATH}/msa.lookup" "${OUTDB}.lookup"
mv -f -- "${TMP_PATH}/msa.source" "${OUTDB}.source"
if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"${MMSEQS}" rmdb "${TMP_PATH}/msa" ${VERB_PAR} \
|| fail "rmdb died"
fi
;;
"GTDB")
# shellcheck disable=SC2086
"${MMSEQS}" tar2db "${TMP_PATH}/gtdb.tar.gz" "${TMP_PATH}/tardb" --tar-include 'faa.gz$' ${THREADS_PAR} \
|| fail "tar2db died"
sed 's|_protein\.faa\.gz||g' "${TMP_PATH}/tardb.lookup" > "${TMP_PATH}/tardb.lookup.tmp"
mv -f -- "${TMP_PATH}/tardb.lookup.tmp" "${TMP_PATH}/tardb.lookup"
# shellcheck disable=SC2086
"${MMSEQS}" createdb "${TMP_PATH}/tardb" "${OUTDB}" ${COMP_PAR} \
|| fail "createdb died"
if [ -n "${REMOVE_TMP}" ]; then
# shellcheck disable=SC2086
"${MMSEQS}" rmdb "${TMP_PATH}/tardb" ${VERB_PAR} \
|| fail "rmdb died"
fi
;;
esac
fi
if [ -n "${TAXONOMY}" ] && notExists "${OUTDB}_mapping"; then
case "${SELECTION}" in
"SILVA")
mkdir -p "${TMP_PATH}/taxonomy"
# shellcheck disable=SC2016
CMD='BEGIN {
ids["root"] = 1;
print "1\t|\t1\t|\tno rank\t|\t-\t|" > taxdir"/nodes.dmp";
print "1\t|\troot\t|\t-\t|\tscientific name\t|" > taxdir"/names.dmp";
}
{
n = split($1, a, ";");
gsub("domain", "superkingdom", $3);
ids[$1] = $2;
gsub(/[^,;]*;$/, "", $1);
pname = $1;
if (n == 2) {
pname = "root";
}
pid = ids[pname];
printf("%s\t|\t%s\t|\t%s\t|\t-\t|\n", $2, pid, $3) > taxdir"/nodes.dmp";
printf("%s\t|\t%s\t|\t-\t|\tscientific name\t|\n", $2, a[n-1]) > taxdir"/names.dmp";
}'
awk -v taxdir="${TMP_PATH}/taxonomy" -F'\t' "$CMD" "${TMP_PATH}/silva_tax.txt"
touch "${TMP_PATH}/taxonomy/merged.dmp"
touch "${TMP_PATH}/taxonomy/delnodes.dmp"
# shellcheck disable=SC2086
"${MMSEQS}" createtaxdb "${OUTDB}" "${TMP_PATH}/taxdb" --ncbi-tax-dump "${TMP_PATH}/taxonomy" --tax-mapping-file "${TMP_PATH}/silva.acc_taxid" ${THREADS_PAR}
;;
"NR")
touch "${OUTDB}_mapping"
# shellcheck disable=SC2086
"${MMSEQS}" createtaxdb "${OUTDB}" "${TMP_PATH}/taxonomy" ${THREADS_PAR} \
|| fail "createtaxdb died"
# shellcheck disable=SC2086
"${MMSEQS}" nrtotaxmapping "${TMP_PATH}/pdb.accession2taxid" "${TMP_PATH}/prot.accession2taxid" "${OUTDB}" "${OUTDB}_mapping" ${THREADS_PAR} \
|| fail "nrtotaxmapping died"
;;
"GTDB")
# shellcheck disable=SC2016
CMD='BEGIN {
FS = "[\t;]";
rank["c"] = "class";
rank["d"] = "superkingdom";
rank["f"] = "family";
rank["g"] = "genus";
rank["o"] = "order";
rank["p"] = "phylum";
rank["s"] = "species";
taxCnt = 1;
ids["root"] = 1;
print "1\t|\t1\t|\tno rank\t|\t-\t|" > taxdir"/nodes.dmp";
print "1\t|\troot\t|\t-\t|\tscientific name\t|" > taxdir"/names.dmp";
}
{
prevTaxon=1;
for (i = 2; i <= NF; i++) {
if ($i in ids) {
prevTaxon = ids[$i];
} else {
taxCnt++;
ids[$i] = taxCnt;
r = substr($i, 0, 1);
name = substr($i, 4);
gsub(/_/, " ", name);
printf("%s\t|\t%s\t|\t%s\t|\t-\t|\n", taxCnt, prevTaxon, rank[r]) > taxdir"/nodes.dmp";
printf("%s\t|\t%s\t|\t-\t|\tscientific name\t|\n", taxCnt, name) > taxdir"/names.dmp";
prevTaxon = taxCnt;
}
}
printf("%s\t%s\n", $1, ids[$NF]) > taxdir"/mapping_genomes";
}'
mkdir -p "${TMP_PATH}/taxonomy"
awk -v taxdir="${TMP_PATH}/taxonomy" "$CMD" "${TMP_PATH}/bac120_taxonomy.tsv" "${TMP_PATH}/ar53_taxonomy.tsv"
touch "${TMP_PATH}/taxonomy/merged.dmp"
touch "${TMP_PATH}/taxonomy/delnodes.dmp"
# shellcheck disable=SC2086
"${MMSEQS}" createtaxdb "${OUTDB}" "${TMP_PATH}/taxdb" --ncbi-tax-dump "${TMP_PATH}/taxonomy" --tax-mapping-file "${TMP_PATH}/taxonomy/mapping_genomes" --tax-mapping-mode 1 ${THREADS_PAR} \
|| fail "createtaxdb died"
if [ -n "${REMOVE_TMP}" ]; then
rm -f -- "${TMP_PATH}/taxonomy/nodes.dmp" "${TMP_PATH}/taxonomy/names.dmp" "${TMP_PATH}/taxonomy/merged.dmp" "${TMP_PATH}/taxonomy/delnodes.dmp" "${TMP_PATH}/taxonomy/mapping_genomes" "${TMP_PATH}/bac120_taxonomy.tsv" "${TMP_PATH}/ar122_taxonomy.tsv"
rm -rf -- "${TMP_PATH}/taxdb" "${TMP_PATH}/taxonomy"
fi
;;
*)
# shellcheck disable=SC2086
"${MMSEQS}" prefixid "${OUTDB}_h" "${TMP_PATH}/header_pref.tsv" --tsv ${THREADS_PAR} \
|| fail "prefixid died"
awk '{ match($0, / OX=[0-9]+ /); if (RLENGTH != -1) { print $1"\t"substr($0, RSTART+4, RLENGTH-5); next; } match($0, / TaxID=[0-9]+ /); print $1"\t"substr($0, RSTART+7, RLENGTH-8); }' "${TMP_PATH}/header_pref.tsv" \
| LC_ALL=C sort -n > "${OUTDB}_mapping"
rm -f "${TMP_PATH}/header_pref.tsv"
# shellcheck disable=SC2086
"${MMSEQS}" createtaxdb "${OUTDB}" "${TMP_PATH}/taxonomy" ${THREADS_PAR} \
|| fail "createtaxdb died"
;;
esac
fi
if notExists "${OUTDB}.version"; then
mv -f "${TMP_PATH}/version" "${OUTDB}.version"
fi
if [ -n "${REMOVE_TMP}" ]; then
rm -f "${TMP_PATH}/download.sh"
fi