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Update Tests for New Linclust #2

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Update Tests for New Linclust #2

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6a2df6b
feat: update regression results
leejoey0921 Sep 2, 2024
6f23b1a
feat: add TC for adjacent=false
leejoey0921 Sep 2, 2024
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2 changes: 1 addition & 1 deletion regression/run_cluster.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ CLUDB="${RESULTS}/clu"

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="15722"
TARGET="15710"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
2 changes: 1 addition & 1 deletion regression/run_cluster_update.sh
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Expand Up @@ -17,7 +17,7 @@ CLUSTERMEMEBER=$(wc -l "$RESULTS/clu_updated.tsv" | awk '{print $1}')
CLUSTER=$(echo $(cut -f1 "$RESULTS/clu_updated.tsv" | sort -u | wc -l))
UPDATEDSEQCNT=$(wc -l "$RESULTS/seqdb_update.index" | awk '{print $1}')

TARGET="32132 24753 32132"
TARGET="32132 24742 32132"
ACTUAL="$CLUSTERMEMEBER $CLUSTER $UPDATEDSEQCNT"
awk -v actual="$ACTUAL" -v target="$TARGET" 'BEGIN { print (actual == target) ? "GOOD" : "BAD"; \
print "Expected: ", target; \
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2 changes: 1 addition & 1 deletion regression/run_easy_cluster.sh
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Expand Up @@ -3,7 +3,7 @@

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="15722"
TARGET="15710"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
2 changes: 1 addition & 1 deletion regression/run_easy_cluster_reassign.sh
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Expand Up @@ -4,7 +4,7 @@ cat "${DATADIR}/clu.fasta" | "${MMSEQS}" easy-cluster stdin "$RESULTS/results"

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="17257"
TARGET="17248"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
2 changes: 1 addition & 1 deletion regression/run_easy_linclust.sh
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Expand Up @@ -3,7 +3,7 @@

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="26493"
TARGET="26146"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
2 changes: 1 addition & 1 deletion regression/run_linclust.sh
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Expand Up @@ -7,7 +7,7 @@ CLUDB=

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="26491"
TARGET="26135"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
13 changes: 13 additions & 0 deletions regression/run_linclust_adjacent_disabled.sh
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@@ -0,0 +1,13 @@
#!/bin/sh -e
CLUDB=
"${MMSEQS}" createdb "${DATADIR}/clu.fasta" "${RESULTS}/clu"

"${MMSEQS}" linclust "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/tmp" --cov-mode 1 --cluster-mode 0 -c 0.90 --min-seq-id 0.50 --match-adjacent-seq false
"${MMSEQS}" createtsv "${RESULTS}/clu" "${RESULTS}/clu" "$RESULTS/results_clu" "$RESULTS/results_cluster.tsv"

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="26491"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
2 changes: 1 addition & 1 deletion regression/run_linclust_split.sh
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Expand Up @@ -6,7 +6,7 @@

awk 'BEGIN { l = "" } l != $1 { l = $1; cnt++; } { t++; } END { print cnt"\t"t"\t"(t/cnt) }' "$RESULTS/results_cluster.tsv" > "$RESULTS/results_summary.tsv"
ACTUAL="$(cut -f1 "$RESULTS/results_summary.tsv")"
TARGET="26491"
TARGET="26135"
awk -v actual="$ACTUAL" -v target="$TARGET" \
'BEGIN { print (actual == target) ? "GOOD" : "BAD"; print "Expected: ", target; print "Actual: ", actual; }' \
> "${RESULTS}.report"
1 change: 1 addition & 0 deletions run_regression.sh
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Expand Up @@ -78,6 +78,7 @@ run_test EASY_CLUSTER "run_easy_cluster.sh"
run_test EASY_NUCL_CLUSTER "run_easy_nuclcluster.sh"
run_test CLUSTER_REASSIGN "run_easy_cluster_reassign.sh"
run_test LINCLUST "run_linclust.sh"
run_test LINCLUST_ADJACENT_DISABLED "run_linclust_adjacent_disabled.sh"
run_test LINCLUST_SPLIT "run_linclust_split.sh"
run_test EASY_LINCLUST "run_easy_linclust.sh"
run_test CLUSTHASH "run_clusthash.sh"
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