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Update obiuniq for very large dataset

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This commit is contained in:
Eric Coissac
2025-12-03 11:48:50 +01:00
parent 547135c747
commit ac0d3f3fe4
10 changed files with 281 additions and 56 deletions
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96
obitests/obitools/obiuniq/test.sh
View File

@@ -98,6 +98,102 @@ else
((failed++))
fi
((ntest++))
if obiuniq "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u.fasta"
then
log "OBIUniq simple: running OK"
((success++))
else
log "OBIUniq simple: running failed"
((failed++))
fi
obicsv -s --auto ${TEST_DIR}/touniq_u.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u_ref.csv"
obicsv -s --auto ${TMPDIR}/touniq_u.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u.csv"
((ntest++))
if diff "${TMPDIR}/touniq_u_ref.csv" \
"${TMPDIR}/touniq_u.csv" > /dev/null
then
log "OBIUniq simple: result OK"
((success++))
else
log "OBIUniq simple: result failed"
((failed++))
fi
((ntest++))
if obiuniq -c a "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_a.fasta"
then
log "OBIUniq one category: running OK"
((success++))
else
log "OBIUniq one category: running failed"
((failed++))
fi
obicsv -s --auto ${TEST_DIR}/touniq_u_a.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u_a_ref.csv"
obicsv -s --auto ${TMPDIR}/touniq_u_a.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u_a.csv"
((ntest++))
if diff "${TMPDIR}/touniq_u_a_ref.csv" \
"${TMPDIR}/touniq_u_a.csv" > /dev/null
then
log "OBIUniq one category: result OK"
((success++))
else
log "OBIUniq one category: result failed"
((failed++))
fi
((ntest++))
if obiuniq -c a -c b "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_a_b.fasta"
then
log "OBIUniq two categories: running OK"
((success++))
else
log "OBIUniq two categories: running failed"
((failed++))
fi
obicsv -s --auto ${TEST_DIR}/touniq_u_a_b.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u_a_b_ref.csv"
obicsv -s --auto ${TMPDIR}/touniq_u_a_b.fasta \
| tail -n +2 \
| sort \
> "${TMPDIR}/touniq_u_a_b.csv"
((ntest++))
if diff "${TMPDIR}/touniq_u_a_b_ref.csv" \
"${TMPDIR}/touniq_u_a_b.csv" > /dev/null
then
log "OBIUniq two categories: result OK"
((success++))
else
log "OBIUniq two categories: result failed"
((failed++))
fi
#########################################
#

16
obitests/obitools/obiuniq/touniq.fasta Normal file
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@@ -0,0 +1,16 @@
>seq1 {"a":2, "b":4,"c":5}
aaacccgggttt
>seq2 {"a":3, "b":4,"c":5}
aaacccgggttt
>seq3 {"a":3, "b":5,"c":5}
aaacccgggttt
>seq4 {"a":3, "b":5,"c":6}
aaacccgggttt
>seq5 {"a":2, "b":4,"c":5}
aaacccgggtttca
>seq6 {"a":3, "b":4,"c":5}
aaacccgggtttca
>seq7 {"a":3, "b":5,"c":5}
aaacccgggtttca
>seq8 {"a":3, "b":5,"c":6}
aaacccgggtttca

4
obitests/obitools/obiuniq/touniq_u.fasta Normal file
View File

@@ -0,0 +1,4 @@
>seq5 {"count":4}
aaacccgggtttca
>seq1 {"count":4}
aaacccgggttt

8
obitests/obitools/obiuniq/touniq_u_a.fasta Normal file
View File

@@ -0,0 +1,8 @@
>seq5 {"a":2,"b":4,"c":5,"count":1}
aaacccgggtttca
>seq6 {"a":3,"count":3}
aaacccgggtttca
>seq1 {"a":2,"b":4,"c":5,"count":1}
aaacccgggttt
>seq2 {"a":3,"count":3}
aaacccgggttt

12
obitests/obitools/obiuniq/touniq_u_a_b.fasta Normal file
View File

@@ -0,0 +1,12 @@
>seq5 {"a":2,"b":4,"c":5,"count":1}
aaacccgggtttca
>seq6 {"a":3,"b":4,"c":5,"count":1}
aaacccgggtttca
>seq7 {"a":3,"b":5,"count":2}
aaacccgggtttca
>seq1 {"a":2,"b":4,"c":5,"count":1}
aaacccgggttt
>seq2 {"a":3,"b":4,"c":5,"count":1}
aaacccgggttt
>seq3 {"a":3,"b":5,"count":2}
aaacccgggttt