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Amandine PERRIN
pipeline_annotation
Commits
c164bc04
Commit
c164bc04
authored
Dec 16, 2021
by
Amandine PERRIN
Browse files
Refseq can have several entries with same strain. Take into account in tests
parent
5a60667c
Pipeline
#71664
failed with stages
in 5 minutes and 14 seconds
Changes
1
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1
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Side-by-side
test/test_functional/test_prepare.py
View file @
c164bc04
...
@@ -231,16 +231,17 @@ def test_main_only_strainname_file():
...
@@ -231,16 +231,17 @@ def test_main_only_strainname_file():
ngd_outdir
=
os
.
path
.
join
(
GENEPATH
,
"refseq"
,
"bacteria"
)
ngd_outdir
=
os
.
path
.
join
(
GENEPATH
,
"refseq"
,
"bacteria"
)
# And that it contains folders
# And that it contains folders
assert
os
.
path
.
isdir
(
ngd_outdir
)
assert
os
.
path
.
isdir
(
ngd_outdir
)
assert
len
(
os
.
listdir
(
ngd_outdir
))
==
3
nbgenomes
=
len
(
os
.
listdir
(
ngd_outdir
))
assert
nbgenomes
>=
3
# Check logfiles are here
# Check logfiles are here
log_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"*log*"
))
log_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"*log*"
))
assert
len
(
log_files
)
==
3
assert
len
(
log_files
)
==
nbgenomes
# Check tmp files folder created, with the 3 strain files
# Check tmp files folder created, with the 3 strain files
tmp_files
=
glob
.
glob
(
os
.
path
.
join
(
tmp_dir
,
"*.fna_prepare-split5N.fna"
))
tmp_files
=
glob
.
glob
(
os
.
path
.
join
(
tmp_dir
,
"*.fna_prepare-split5N.fna"
))
assert
len
(
tmp_files
)
==
3
assert
len
(
tmp_files
)
==
nbgenomes
# Check Database_init folder created, with all 3 ".fna" genomes
# Check Database_init folder created, with all 3 ".fna" genomes
fna_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"Database_init"
,
"*.fna"
))
fna_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"Database_init"
,
"*.fna"
))
assert
len
(
fna_files
)
==
3
assert
len
(
fna_files
)
==
nbgenomes
def
test_main_not_only_mash_infoexists
():
def
test_main_not_only_mash_infoexists
():
...
...
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