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Merge pull request #353 from rachelse/master
Multimer cluster
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,163 @@ | ||
| #!/bin/sh -e | ||
| fail() { | ||
| echo "Error: $1" | ||
| exit 1 | ||
| } | ||
|
|
||
| notExists() { | ||
| [ ! -f "$1" ] | ||
| } | ||
|
|
||
| exists() { | ||
| [ -f "$1" ] | ||
| } | ||
|
|
||
| abspath() { | ||
| if [ -d "$1" ]; then | ||
| (cd "$1"; pwd) | ||
| elif [ -f "$1" ]; then | ||
| if [ -z "${1##*/*}" ]; then | ||
| echo "$(cd "${1%/*}"; pwd)/${1##*/}" | ||
| else | ||
| echo "$(pwd)/$1" | ||
| fi | ||
| elif [ -d "$(dirname "$1")" ]; then | ||
| echo "$(cd "$(dirname "$1")"; pwd)/$(basename "$1")" | ||
| fi | ||
| } | ||
|
|
||
| mapCmplName2ChainKeys() { | ||
| awk -F"\t" 'FNR==1 {++fIndex} | ||
| fIndex==1 { | ||
| repName[$1]=1 | ||
| if (match($1, /MODEL/)){ | ||
| tmpName[$1]=1 | ||
| }else{ | ||
| tmpName[$1"_MODEL_1"]=1 | ||
| } | ||
| next | ||
| } | ||
| fIndex==2{ | ||
| if (match($2, /MODEL/)){ | ||
| if ($2 in tmpName){ | ||
| repId[$1]=1 | ||
| }else{ | ||
| ho[1]=1 | ||
| } | ||
| }else{ | ||
| if ($2 in repName){ | ||
| repId[$1]=1 | ||
| } | ||
| } | ||
| next | ||
| } | ||
| { | ||
| if ($3 in repId){ | ||
| print $1 | ||
| } | ||
| } | ||
| ' "${1}" "${2}.source" "${2}.lookup" > "${3}" | ||
| } | ||
|
|
||
| postprocessFasta() { | ||
| awk ' BEGIN {FS=">"} | ||
| $0 ~/^>/ { | ||
| # match($2, /(.*).pdb*/) | ||
| split($2,parts,"_") | ||
| complex="" | ||
| for (j = 1; j < length(parts); j++) { | ||
| complex = complex parts[j] | ||
| if (j < length(parts)-1){ | ||
| complex=complex"_" | ||
| } | ||
| } | ||
| if (!(complex in repComplex)) { | ||
| print "#"complex | ||
| repComplex[complex] = "" | ||
| } | ||
| } | ||
| {print $0} | ||
| ' "${1}" > "${1}.tmp" && mv "${1}.tmp" "${1}" | ||
| } | ||
|
|
||
| if notExists "${TMP_PATH}/query.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" createdb "${INPUT}" "${TMP_PATH}/query" ${CREATEDB_PAR} \ | ||
| || fail "query createdb died" | ||
| fi | ||
|
|
||
| if notExists "${TMP_PATH}/multimer_clu.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" multimercluster "${TMP_PATH}/query" "${TMP_PATH}/multimer_clu" "${TMP_PATH}" ${MULTIMERCLUSTER_PAR} \ | ||
| || fail "Multimercluster died" | ||
| fi | ||
|
|
||
| SOURCE="${TMP_PATH}/query" | ||
| INPUT="${TMP_PATH}/latest/multimer_db" | ||
| if notExists "${TMP_PATH}/cluster.tsv"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" createtsv "${INPUT}" "${INPUT}" "${TMP_PATH}/multimer_clu" "${TMP_PATH}/cluster.tsv" ${THREADS_PAR} \ | ||
| || fail "Convert Alignments died" | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" createtsv "${INPUT}" "${INPUT}" "${TMP_PATH}/multimer_clu_filt_info" "${TMP_PATH}/cluster_report" ${THREADS_PAR} \ | ||
| || fail "Convert Alignments died" | ||
| fi | ||
|
|
||
| if notExists "${TMP_PATH}/multimer_rep_seqs.dbtype"; then | ||
| mapCmplName2ChainKeys "${TMP_PATH}/cluster.tsv" "${SOURCE}" "${TMP_PATH}/rep_seqs.list" | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" createsubdb "${TMP_PATH}/rep_seqs.list" "${SOURCE}" "${TMP_PATH}/multimer_rep_seqs" ${CREATESUBDB_PAR} \ | ||
| || fail "createsubdb died" | ||
| fi | ||
|
|
||
| if notExists "${TMP_PATH}/multimer_rep_seq.fasta"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" result2flat "${SOURCE}" "${SOURCE}" "${TMP_PATH}/multimer_rep_seqs" "${TMP_PATH}/multimer_rep_seq.fasta" ${VERBOSITY_PAR} \ | ||
| || fail "result2flat died" | ||
| postprocessFasta "${TMP_PATH}/multimer_rep_seq.fasta" | ||
| fi | ||
|
|
||
| #TODO: generate fasta file for all sequences | ||
| # if notExists "${TMP_PATH}/multimer_all_seqs.fasta"; then | ||
| # # shellcheck disable=SC2086 | ||
| # "$MMSEQS" createseqfiledb "${INPUT}" "${TMP_PATH}/multimer_clu" "${TMP_PATH}/multimer_clust_seqs" ${THREADS_PAR} \ | ||
| # || fail "Result2repseq died" | ||
|
|
||
| # # shellcheck disable=SC2086 | ||
| # "$MMSEQS" result2flat "${INPUT}" "${INPUT}" "${TMP_PATH}/multimer_clust_seqs" "${TMP_PATH}/multimer_all_seqs.fasta" ${VERBOSITY_PAR} \ | ||
| # || fail "result2flat died" | ||
| # fi | ||
|
|
||
| # mv "${TMP_PATH}/multimer_all_seqs.fasta" "${RESULT}_all_seqs.fasta" | ||
| mv "${TMP_PATH}/multimer_rep_seq.fasta" "${RESULT}_rep_seq.fasta" | ||
| mv "${TMP_PATH}/cluster.tsv" "${RESULT}_cluster.tsv" | ||
| mv "${TMP_PATH}/cluster_report" "${RESULT}_cluster_report" | ||
|
|
||
| if [ -n "${REMOVE_TMP}" ]; then | ||
| rm "${INPUT}.0" | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/multimer_db" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| # "$MMSEQS" rmdb "${TMP_PATH}/multimer_clu_seqs" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/multimer_rep_seqs" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/multimer_rep_seqs_h" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/complex_clu" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/query" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/query_h" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${INPUT}" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${INPUT}_h" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/query_ca" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/query_ss" ${VERBOSITY_PAR} | ||
| rm "${TMP_PATH}/rep_seqs.list" | ||
| rm -rf "${TMP_PATH}/latest" | ||
| rm -f "${TMP_PATH}/easymultimercluster.sh" | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| #!/bin/sh -e | ||
| fail() { | ||
| echo "Error: $1" | ||
| exit 1 | ||
| } | ||
|
|
||
| notExists() { | ||
| [ ! -f "$1" ] | ||
| } | ||
|
|
||
| exists() { | ||
| [ -f "$1" ] | ||
| } | ||
|
|
||
| abspath() { | ||
| if [ -d "$1" ]; then | ||
| (cd "$1"; pwd) | ||
| elif [ -f "$1" ]; then | ||
| if [ -z "${1##*/*}" ]; then | ||
| echo "$(cd "${1%/*}"; pwd)/${1##*/}" | ||
| else | ||
| echo "$(pwd)/$1" | ||
| fi | ||
| elif [ -d "$(dirname "$1")" ]; then | ||
| echo "$(cd "$(dirname "$1")"; pwd)/$(basename "$1")" | ||
| fi | ||
| } | ||
|
|
||
| # Shift initial DB to complexDB using soft-linking | ||
| # $1: input db | ||
| # $2: output db | ||
| buildCmplDb() { | ||
| touch "${2}" | ||
| awk -F"\t" 'BEGIN {OFFSET=0} | ||
| FNR==NR{chain_len[$1]=$3;next} | ||
| { | ||
| if (!($3 in off_arr)) { | ||
| off_arr[$3]=OFFSET | ||
| } | ||
| cmpl_len[$3]+=chain_len[$1];OFFSET+=chain_len[$1] | ||
| } | ||
| END { | ||
| for (cmpl in off_arr) { | ||
| print cmpl"\t"off_arr[cmpl]"\t"cmpl_len[cmpl] | ||
| } | ||
| }' "${1}.index" "${1}.lookup" > "${2}.index" | ||
| ln -s "$(abspath "${1}")" "${2}.0" | ||
| cp "${1}.dbtype" "${2}.dbtype" | ||
| } | ||
|
|
||
| buldCmplhDb(){ | ||
| awk -F"\t" 'BEGIN {INDEXVAL=0} | ||
| { | ||
| split($2,words," ") | ||
| split(words[1],parts,"_") | ||
| output_string=parts[1] | ||
| for (j = 2; j < length(parts); j++) { | ||
| if (j < length(parts)){ | ||
| output_string=output_string"_" | ||
| } | ||
| output_string = output_string parts[j] | ||
| } | ||
| headerstring="" | ||
| for (k = 2; k < length(words)+1; k++) { | ||
| headerstring = headerstring words[k]" " | ||
| } | ||
| if (!(output_string in gogo)){ | ||
| print INDEXVAL"\t"output_string" "headerstring | ||
| INDEXVAL++ | ||
| } | ||
| gogo[output_string]=1 | ||
| }' "${1}" > "${2}" | ||
| } | ||
|
|
||
|
|
||
| # [ ! -d "$3" ] && echo "tmp directory $3 not found!" && mkdir -p "${TMP_PATH}"; | ||
|
|
||
| if notExists "${TMP_PATH}/multimer_result.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" multimersearch "${INPUT}" "${INPUT}" "${TMP_PATH}/multimer_result" "${TMP_PATH}/multimersearch_tmp" ${MULTIMERSEARCH_PAR} \ | ||
| || fail "multimerSearch died" | ||
| fi | ||
|
|
||
| if notExists "multimer_filt.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" filtermultimer "${INPUT}" "${INPUT}" "${TMP_PATH}/multimer_result" "${TMP_PATH}/multimer_filt" ${FILTERMULTIMER_PAR} \ | ||
| || fail "FilterMultimer died" | ||
| fi | ||
|
|
||
| # shift query DB, .index, .dbtype | ||
| if notExists "${TMP_PATH}/multimer_db.dbtype"; then | ||
| # build complex db as output | ||
| buildCmplDb "${INPUT}" "${TMP_PATH}/multimer_db" | ||
| fi | ||
|
|
||
| # Shift _h, _h.dbtype | ||
| if notExists "${TMP_PATH}/multimer_db_h.dbtype"; then | ||
| # # shellcheck disable=SC2086 | ||
| # "$MMSEQS" tsv2db "${INPUT}.source" "${TMP_PATH}/complex_db_header_tmp" ${VERBOSITY_PAR} \ | ||
| # || fail "tsv2db died" | ||
| # shellcheck disable=SC2086 | ||
| # "$MMSEQS" createtsv "${INPUT}" "${INPUT}_h" "${TMP_PATH}/chain_db_h.tsv" ${VERBOSITY_PAR} \ | ||
| "$MMSEQS" createtsv "${INPUT}" "${INPUT}_h" "${TMP_PATH}/chain_db_h.tsv" --threads 1 \ | ||
| || fail "createtsv died" | ||
| buldCmplhDb "${TMP_PATH}/chain_db_h.tsv" "${TMP_PATH}/multimer_header.tsv" | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" tsv2db "${TMP_PATH}/multimer_header.tsv" "${TMP_PATH}/multimer_db_h" ${VERBOSITY_PAR} \ | ||
| || fail "tsv2db died" | ||
| fi | ||
|
|
||
| COMP="${TMP_PATH}/multimer_db" | ||
|
|
||
| if notExists "${RESULT}.dbtype"; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" clust "${COMP}" "${TMP_PATH}/multimer_filt" "${RESULT}" ${CLUSTER_PAR} \ | ||
| || fail "Clustering died" | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" mvdb "${TMP_PATH}/multimer_filt_info" "${RESULT}_filt_info" \ | ||
| || fail "mv died" | ||
|
|
||
| fi | ||
|
|
||
| if [ -n "${REMOVE_TMP}" ]; then | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/multimer_filt" ${VERBOSITY_PAR} | ||
| # shellcheck disable=SC2086 | ||
| "$MMSEQS" rmdb "${TMP_PATH}/multimer_result" ${VERBOSITY_PAR} | ||
| rm "${TMP_PATH}/chain_db_h.tsv" | ||
| rm "${TMP_PATH}/multimer_header.tsv" | ||
| rm -rf "${TMP_PATH}/multimersearch_tmp" | ||
| rm -f "${TMP_PATH}/multimercluster.sh" | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -124,5 +124,4 @@ class BasicFunction{ | |
| // transform(t, u, x.x[i], x.y[i], x.z[i], y.x[i], y.y[i], y.z[i]); | ||
| } | ||
| } | ||
|
|
||
| }; | ||
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