sokrypton / sokrypton/ColabFold
Trouble using pair.sh
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Description
Hello,
The pair.sh generated by api server is as follows:
#!/bin/bash -e
MMSEQS="$1"
QUERY="$2"
BASE="$4"
DB1="$5"
USE_PAIRWISE="$6"
SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a --k-score 'seq:96,prof:80' -e 0.1 --max-seqs 10000"
EXPAND_PARAM="--expansion-mode 0 -e inf --expand-filter-clusters 0 --max-seq-id 0.95"
export MMSEQS_CALL_DEPTH=1
"${MMSEQS}" createdb "${QUERY}" "${BASE}/qdb" --shuffle 0
"${MMSEQS}" search "${BASE}/qdb" "${DB1}" "${BASE}/res" "${BASE}/tmp" $SEARCH_PARAM
if [ "${USE_PAIRWISE}" = "1" ]; then
for i in qdb res qdb_h; do
awk 'BEGIN { OFS="\t"; cnt = 0; } NR == 1 { off = $2; len = $3; next; } { print (2*cnt),off,len; print (2*cnt)+1,$2,$3; cnt+=1; }' "${BASE}/${i}.index" > "${BASE}/${i}.index_tmp"
mv -f -- "${BASE}/${i}.index_tmp" "${BASE}/${i}.index"
done
# write a new qdb.lookup to enable pairwise pairing
awk 'BEGIN { OFS="\t"; cnt = 0; } NR == 1 { off = $2; len = $3; next; } { print (2*cnt),off,cnt; print (2*cnt)+1,$2,cnt; cnt+=1; }' "${BASE}/qdb.lookup" > "${BASE}/qdb.lookup_tmp"
mv -f -- "${BASE}/qdb.lookup_tmp" "${BASE}/qdb.lookup"
fi
"${MMSEQS}" expandaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res" "${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM}
"${MMSEQS}" align "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode 2 -e 0.001 --max-accept 1000000 -c 0.5 --cov-mode 1
"${MMSEQS}" pairaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_pair" --db-load-mode 2
"${MMSEQS}" align "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_pair" "${BASE}/res_exp_realign_pair_bt" --db-load-mode 2 -e inf -a
"${MMSEQS}" pairaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_pair_bt" "${BASE}/res_final" --db-load-mode 2
"${MMSEQS}" result2msa "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_final" "${BASE}/pair.a3m" --db-load-mode 2 --msa-format-mode 5
"${MMSEQS}" rmdb "${BASE}/qdb"
"${MMSEQS}" rmdb "${BASE}/qdb_h"
"${MMSEQS}" rmdb "${BASE}/res"
"${MMSEQS}" rmdb "${BASE}/res_exp"
"${MMSEQS}" rmdb "${BASE}/res_exp_realign"
"${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair"
"${MMSEQS}" rmdb "${BASE}/res_exp_realign_pair_bt"
"${MMSEQS}" rmdb "${BASE}/res_final"
rm -rf -- "${BASE}/tmp"
What's the DB1?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the generated pair.sh shown in the report and trace the API-server input associated with the DB1 variable. Check the project documentation for the expected database value and explain where it comes from. Done when users can identify DB1 without reverse-engineering the generated script.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- bash
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100