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Add a new test on obisummary

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This commit is contained in:
Eric Coissac
2025-07-07 15:28:29 +02:00
parent 235a7e202a
commit 8c26fc9884
4 changed files with 112 additions and 0 deletions
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9
obitests/obitools/obisummary/some_uniq_seq.fasta Normal file
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@@ -0,0 +1,9 @@
>Seq_1 {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agctyaaaactcaaaggacttggcggtgctttataccctt
>Seq_2 {"count":22,"merged_sample":{"15a_F730814":12,"29a_F260619":10}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
atcttaaaactcaaaggacttggcggtgctttataccctt
>Seq_3 {"count":22,"merged_sample":{"15a_F730814":15,"29a_F260619":7}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
agcttaaaactcaaaggacttggcggtgctttataccctt

35
obitests/obitools/obisummary/some_uniq_seq.json Normal file
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@@ -0,0 +1,35 @@
{
"annotations": {
"keys": {
"map": {
"merged_sample": 3
},
"scalar": {
"count": 3
}
},
"map_attributes": 1,
"scalar_attributes": 1,
"vector_attributes": 0
},
"count": {
"reads": 46,
"total_length": 300,
"variants": 3
},
"samples": {
"sample_count": 2,
"sample_stats": {
"15a_F730814": {
"reads": 28,
"singletons": 1,
"variants": 3
},
"29a_F260619": {
"reads": 18,
"singletons": 1,
"variants": 3
}
}
}
}

25
obitests/obitools/obisummary/some_uniq_seq.yaml Normal file
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@@ -0,0 +1,25 @@
annotations:
keys:
map:
merged_sample: 3
scalar:
count: 3
map_attributes: 1
scalar_attributes: 1
vector_attributes: 0
count:
reads: 46
total_length: 300
variants: 3
samples:
sample_count: 2
sample_stats:
15a_F730814:
reads: 28
singletons: 1
variants: 3
29a_F260619:
reads: 18
singletons: 1
variants: 3

43
obitests/obitools/obisummary/test.sh
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@@ -98,6 +98,49 @@ else
((failed++)) ((failed++))
fi fi
((ntest++))
if obisummary "${TEST_DIR}/some_uniq_seq.fasta" \
> "${TMPDIR}/some_uniq_seq.json"
then
log "$MCMD: formating json execution OK"
((success++))
else
log "$MCMD: formating json execution failed"
((failed++))
fi
((ntest++))
if diff "${TEST_DIR}/some_uniq_seq.json" \
"${TMPDIR}/some_uniq_seq.json" > /dev/null
then
log "$MCMD: formating json OK"
((success++))
else
log "$MCMD: formating json failed"
((failed++))
fi
((ntest++))
if obisummary --yaml "${TEST_DIR}/some_uniq_seq.fasta" \
> "${TMPDIR}/some_uniq_seq.yaml"
then
log "$MCMD: formating yaml execution OK"
((success++))
else
log "$MCMD: formating yaml execution failed"
((failed++))
fi
((ntest++))
if diff "${TEST_DIR}/some_uniq_seq.yaml" \
"${TMPDIR}/some_uniq_seq.yaml" > /dev/null
then
log "$MCMD: formating yaml OK"
((success++))
else
log "$MCMD: formating yaml failed"
((failed++))
fi
######################################### #########################################
# #