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Amandine PERRIN
panacota
Commits
c8ce71c0
Commit
c8ce71c0
authored
3 years ago
by
Amandine PERRIN
Browse files
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Adapt functional tests for new feature in prepare
parent
f5469400
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2 changed files
PanACoTA/subcommands/prepare.py
+3
-1
3 additions, 1 deletion
PanACoTA/subcommands/prepare.py
test/test_functional/test_prepare.py
+130
-23
130 additions, 23 deletions
test/test_functional/test_prepare.py
with
133 additions
and
24 deletions
PanACoTA/subcommands/prepare.py
+
3
−
1
View file @
c8ce71c0
...
@@ -155,9 +155,11 @@ def main(cmd, ncbi_species_name, ncbi_species_taxid, ncbi_taxid, ncbi_strains, l
...
@@ -155,9 +155,11 @@ def main(cmd, ncbi_species_name, ncbi_species_taxid, ncbi_taxid, ncbi_strains, l
elif
ncbi_strains
:
elif
ncbi_strains
:
if
os
.
path
.
isfile
(
ncbi_strains
):
if
os
.
path
.
isfile
(
ncbi_strains
):
species_linked
=
os
.
path
.
basename
(
ncbi_strains
)
species_linked
=
os
.
path
.
basename
(
ncbi_strains
)
species_linked
=
os
.
path
.
splitext
(
species_linked
)[
0
]
else
:
else
:
species_linked
=
"
_
"
.
join
(
ncbi_strains
.
split
())
species_linked
=
"
_
"
.
join
(
ncbi_strains
.
split
())
species_linked
=
"
-
"
.
join
(
ncbi_strains
.
split
(
"
/
"
))
species_linked
=
"
-
"
.
join
(
species_linked
.
split
(
"
/
"
))
species_linked
=
"
_and_
"
.
join
(
species_linked
.
split
(
"
,
"
))
# if neither speName, speID, taxID nor strainName given (--norefseq, mashonly), name is NA
# if neither speName, speID, taxID nor strainName given (--norefseq, mashonly), name is NA
else
:
else
:
species_linked
=
"
NA
"
species_linked
=
"
NA
"
...
...
This diff is collapsed.
Click to expand it.
test/test_functional/test_prepare.py
+
130
−
23
View file @
c8ce71c0
...
@@ -58,6 +58,7 @@ def test_main_from_parse():
...
@@ -58,6 +58,7 @@ def test_main_from_parse():
args
.
ncbi_species_name
=
"
Acetobacter orleanensis
"
args
.
ncbi_species_name
=
"
Acetobacter orleanensis
"
args
.
ncbi_species_taxid
=
"
104099
"
args
.
ncbi_species_taxid
=
"
104099
"
args
.
ncbi_taxid
=
""
args
.
ncbi_taxid
=
""
args
.
strains
=
""
args
.
ncbi_section
=
"
refseq
"
args
.
ncbi_section
=
"
refseq
"
args
.
outdir
=
GENEPATH
args
.
outdir
=
GENEPATH
args
.
tmp_dir
=
""
args
.
tmp_dir
=
""
...
@@ -105,6 +106,7 @@ def test_main_from_parse_longspeciesname():
...
@@ -105,6 +106,7 @@ def test_main_from_parse_longspeciesname():
args
.
ncbi_species_name
=
"
Salmonella enterica subsp. enterica serovar Paratyphi C
"
args
.
ncbi_species_name
=
"
Salmonella enterica subsp. enterica serovar Paratyphi C
"
args
.
ncbi_species_taxid
=
""
args
.
ncbi_species_taxid
=
""
args
.
ncbi_taxid
=
""
args
.
ncbi_taxid
=
""
args
.
strains
=
""
args
.
ncbi_section
=
"
refseq
"
args
.
ncbi_section
=
"
refseq
"
args
.
outdir
=
GENEPATH
args
.
outdir
=
GENEPATH
args
.
tmp_dir
=
""
args
.
tmp_dir
=
""
...
@@ -143,6 +145,104 @@ def test_main_from_parse_longspeciesname():
...
@@ -143,6 +145,104 @@ def test_main_from_parse_longspeciesname():
assert
len
(
fna_files
)
>=
1
assert
len
(
fna_files
)
>=
1
def
test_main_only_strainname
():
"""
Only give strain names (no spe taxid etc). Chack that they are downloaded,
and that the summary file has the expected name.
"""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_section
=
"
refseq
"
NCBI_strains
=
"
AS001254,KPPR1,LMG 1583
"
levels
=
""
outdir
=
GENEPATH
tmp_dir
=
os
.
path
.
join
(
outdir
,
'
tmp
'
)
threads
=
1
norefseq
=
False
db_dir
=
""
only_mash
=
False
info_file
=
""
l90
=
100
nbcont
=
999
cutn
=
5
min_dist
=
1e-4
max_dist
=
0.06
verbose
=
2
quiet
=
False
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-AS001254_and_KPPR1_and_LMG_1583-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
# Check output files
summary
=
os
.
path
.
join
(
GENEPATH
,
"
assembly_summary-AS001254_and_KPPR1_and_LMG_1583.txt
"
)
assert
os
.
path
.
isfile
(
summary
)
# Check that the NCBI_genome_download output directory exists
ngd_outdir
=
os
.
path
.
join
(
GENEPATH
,
"
refseq
"
,
"
bacteria
"
)
# And that it contains folders
assert
os
.
path
.
isdir
(
ngd_outdir
)
assert
len
(
os
.
listdir
(
ngd_outdir
))
==
3
# Check logfiles are here
log_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"
*log*
"
))
assert
len
(
log_files
)
==
3
# Check tmp files folder created, with the 3 strain files
tmp_files
=
glob
.
glob
(
os
.
path
.
join
(
tmp_dir
,
"
*.fna_prepare-split5N.fna
"
))
assert
len
(
tmp_files
)
==
3
# Check Database_init folder created, with all 3 ".fna" genomes
fna_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"
Database_init
"
,
"
*.fna
"
))
assert
len
(
fna_files
)
==
3
def
test_main_only_strainname_file
():
"""
Only give strain names (no spe taxid etc). Chack that they are downloaded,
and that the summary file has the expected name.
"""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_section
=
"
refseq
"
NCBI_strains
=
os
.
path
.
join
(
TEST_DIR
,
"
test_list-strains.txt
"
)
levels
=
""
outdir
=
GENEPATH
tmp_dir
=
os
.
path
.
join
(
outdir
,
'
tmp
'
)
threads
=
1
norefseq
=
False
db_dir
=
""
only_mash
=
False
info_file
=
""
l90
=
100
nbcont
=
999
cutn
=
5
min_dist
=
1e-4
max_dist
=
0.06
verbose
=
2
quiet
=
False
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-test_list-strains-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
# Check output files
summary
=
os
.
path
.
join
(
GENEPATH
,
"
assembly_summary-test_list-strains.txt
"
)
assert
os
.
path
.
isfile
(
summary
)
# Check that the NCBI_genome_download output directory exists
ngd_outdir
=
os
.
path
.
join
(
GENEPATH
,
"
refseq
"
,
"
bacteria
"
)
# And that it contains folders
assert
os
.
path
.
isdir
(
ngd_outdir
)
assert
len
(
os
.
listdir
(
ngd_outdir
))
==
3
# Check logfiles are here
log_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"
*log*
"
))
assert
len
(
log_files
)
==
3
# Check tmp files folder created, with the 3 strain files
tmp_files
=
glob
.
glob
(
os
.
path
.
join
(
tmp_dir
,
"
*.fna_prepare-split5N.fna
"
))
assert
len
(
tmp_files
)
==
3
# Check Database_init folder created, with all 3 ".fna" genomes
fna_files
=
glob
.
glob
(
os
.
path
.
join
(
GENEPATH
,
"
Database_init
"
,
"
*.fna
"
))
assert
len
(
fna_files
)
==
3
def
test_main_not_only_mash_infoexists
():
def
test_main_not_only_mash_infoexists
():
"""
"""
We run without option only_mash, but still provide a lstinfo file
We run without option only_mash, but still provide a lstinfo file
...
@@ -152,6 +252,7 @@ def test_main_not_only_mash_infoexists():
...
@@ -152,6 +252,7 @@ def test_main_not_only_mash_infoexists():
NCBI_species_taxid
=
"
104099
"
NCBI_species_taxid
=
"
104099
"
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
NCBI_strains
=
""
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
tmp_dir
=
os
.
path
.
join
(
outdir
,
"
temporary_directory
"
)
tmp_dir
=
os
.
path
.
join
(
outdir
,
"
temporary_directory
"
)
...
@@ -169,7 +270,7 @@ def test_main_not_only_mash_infoexists():
...
@@ -169,7 +270,7 @@ def test_main_not_only_mash_infoexists():
verbose
=
2
verbose
=
2
quiet
=
False
quiet
=
False
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-104099-filtered-0.0001_0.06.txt
"
)
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-104099-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
...
@@ -204,10 +305,11 @@ def test_main_wrong_taxid(capsys):
...
@@ -204,10 +305,11 @@ def test_main_wrong_taxid(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_taxid
=
"
123
"
NCBI_taxid
=
"
123
"
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
genbank
"
NCBI_section
=
"
genbank
"
levels
=
""
levels
=
""
outdir
=
""
outdir
=
GENEPATH
tmp_dir
=
os
.
path
.
join
(
"
123
"
,
"
temporary_directory
"
)
tmp_dir
=
os
.
path
.
join
(
GENEPATH
,
"
123
"
,
"
temporary_directory
"
)
threads
=
1
threads
=
1
norefseq
=
False
norefseq
=
False
info_file
=
""
info_file
=
""
...
@@ -220,31 +322,28 @@ def test_main_wrong_taxid(capsys):
...
@@ -220,31 +322,28 @@ def test_main_wrong_taxid(capsys):
max_dist
=
0.06
max_dist
=
0.06
verbose
=
2
verbose
=
2
quiet
=
False
quiet
=
False
res_outdir
=
"
123
"
with
pytest
.
raises
(
SystemExit
):
with
pytest
.
raises
(
SystemExit
):
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
NCBI_section
,
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
verbose
,
quiet
)
_
,
err
=
capsys
.
readouterr
()
_
,
err
=
capsys
.
readouterr
()
assert
(
"
Could not download genomes. Check that you gave valid NCBI taxid and/or
"
assert
(
"
No strain correspond to your request. If you are sure there should have
"
"
NCBI species name. If you gave both, check that given taxID and name really
"
"
some, check that you gave valid NCBI taxid and/or
"
"
correspond to the same species.
"
)
in
err
"
NCBI species name and/or NCBI strain name. If you gave several, check that
"
"
given taxIDs and names are compatible.
"
)
in
err
# Check output files
# Check output files
summary
=
os
.
path
.
join
(
res_
outdir
,
"
assembly_summary-123.txt
"
)
summary
=
os
.
path
.
join
(
outdir
,
"
assembly_summary-123.txt
"
)
assert
not
os
.
path
.
isfile
(
summary
)
assert
not
os
.
path
.
isfile
(
summary
)
ngd_outdir
=
os
.
path
.
join
(
res_
outdir
,
"
genbank
"
,
"
bacteria
"
)
ngd_outdir
=
os
.
path
.
join
(
outdir
,
"
genbank
"
,
"
bacteria
"
)
assert
not
os
.
path
.
isdir
(
ngd_outdir
)
assert
not
os
.
path
.
isdir
(
ngd_outdir
)
# # Check logfiles are here
# # Check logfiles are here
log_files
=
glob
.
glob
(
os
.
path
.
join
(
res_
outdir
,
"
*log*
"
))
log_files
=
glob
.
glob
(
os
.
path
.
join
(
outdir
,
"
*log*
"
))
assert
len
(
log_files
)
==
3
assert
len
(
log_files
)
==
3
# Check tmp files folder created, but empty asnothing is downloaded
# Check tmp files folder created, but empty asnothing is downloaded
assert
len
(
os
.
listdir
(
tmp_dir
))
==
0
assert
len
(
os
.
listdir
(
tmp_dir
))
==
0
# Check Database_init folder created, with at list 4 ".fna" genomes
# Check Database_init folder created, with at list 4 ".fna" genomes
assert
not
os
.
path
.
isdir
(
os
.
path
.
join
(
res_outdir
,
"
Database_init
"
))
assert
not
os
.
path
.
isdir
(
os
.
path
.
join
(
outdir
,
"
Database_init
"
))
# Remove output directory
shutil
.
rmtree
(
res_outdir
,
ignore_errors
=
True
)
def
test_main_norefseq_wrongdbpath
(
capsys
):
def
test_main_norefseq_wrongdbpath
(
capsys
):
...
@@ -255,6 +354,7 @@ def test_main_norefseq_wrongdbpath(capsys):
...
@@ -255,6 +354,7 @@ def test_main_norefseq_wrongdbpath(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
...
@@ -272,7 +372,7 @@ def test_main_norefseq_wrongdbpath(capsys):
...
@@ -272,7 +372,7 @@ def test_main_norefseq_wrongdbpath(capsys):
quiet
=
False
quiet
=
False
info_file
=
""
info_file
=
""
with
pytest
.
raises
(
SystemExit
):
with
pytest
.
raises
(
SystemExit
):
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
NCBI_section
,
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
verbose
,
quiet
)
...
@@ -302,6 +402,7 @@ def test_main_norefseq_nodefault_dbdir_nor_refseq(capsys):
...
@@ -302,6 +402,7 @@ def test_main_norefseq_nodefault_dbdir_nor_refseq(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
genbank
"
NCBI_section
=
"
genbank
"
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
...
@@ -319,7 +420,7 @@ def test_main_norefseq_nodefault_dbdir_nor_refseq(capsys):
...
@@ -319,7 +420,7 @@ def test_main_norefseq_nodefault_dbdir_nor_refseq(capsys):
quiet
=
False
quiet
=
False
info_file
=
""
info_file
=
""
with
pytest
.
raises
(
SystemExit
):
with
pytest
.
raises
(
SystemExit
):
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
verbose
,
quiet
)
...
@@ -359,6 +460,7 @@ def test_main_norefseq_nodefault_dbdir_but_refseq(capsys):
...
@@ -359,6 +460,7 @@ def test_main_norefseq_nodefault_dbdir_but_refseq(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
"
123
"
NCBI_species_taxid
=
"
123
"
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
genbank
"
NCBI_section
=
"
genbank
"
levels
=
""
levels
=
""
# Copy refseq/bacteria and content into outdirectory
# Copy refseq/bacteria and content into outdirectory
...
@@ -380,7 +482,7 @@ def test_main_norefseq_nodefault_dbdir_but_refseq(capsys):
...
@@ -380,7 +482,7 @@ def test_main_norefseq_nodefault_dbdir_but_refseq(capsys):
quiet
=
False
quiet
=
False
info_file
=
""
info_file
=
""
out_info_file
=
os
.
path
.
join
(
outdir
,
f
"
LSTINFO-123-filtered-0.0001_0.06.txt
"
)
out_info_file
=
os
.
path
.
join
(
outdir
,
f
"
LSTINFO-123-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
max_dist
,
verbose
,
quiet
)
==
out_info_file
...
@@ -419,6 +521,7 @@ def test_main_norefseq_defaultdbdir(capsys):
...
@@ -419,6 +521,7 @@ def test_main_norefseq_defaultdbdir(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
# Copy refseq/bacteria and content into outdirectory
# Copy refseq/bacteria and content into outdirectory
...
@@ -440,7 +543,7 @@ def test_main_norefseq_defaultdbdir(capsys):
...
@@ -440,7 +543,7 @@ def test_main_norefseq_defaultdbdir(capsys):
quiet
=
False
quiet
=
False
info_file
=
""
info_file
=
""
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
max_dist
,
verbose
,
quiet
)
==
out_info_file
...
@@ -472,6 +575,7 @@ def test_main_norefseq_givendbdir(capsys):
...
@@ -472,6 +575,7 @@ def test_main_norefseq_givendbdir(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
# Copy refseq/bacteria and content into outdirectory
# Copy refseq/bacteria and content into outdirectory
...
@@ -493,7 +597,7 @@ def test_main_norefseq_givendbdir(capsys):
...
@@ -493,7 +597,7 @@ def test_main_norefseq_givendbdir(capsys):
quiet
=
False
quiet
=
False
info_file
=
""
info_file
=
""
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
max_dist
,
verbose
,
quiet
)
==
out_info_file
...
@@ -521,6 +625,7 @@ def test_only_mash(capsys):
...
@@ -521,6 +625,7 @@ def test_only_mash(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
...
@@ -538,7 +643,7 @@ def test_only_mash(capsys):
...
@@ -538,7 +643,7 @@ def test_only_mash(capsys):
verbose
=
1
verbose
=
1
quiet
=
False
quiet
=
False
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
out_info_file
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-NA-filtered-0.0001_0.06.txt
"
)
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
assert
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
==
out_info_file
max_dist
,
verbose
,
quiet
)
==
out_info_file
...
@@ -569,6 +674,7 @@ def test_only_mash_empty_lstinfo(capsys):
...
@@ -569,6 +674,7 @@ def test_only_mash_empty_lstinfo(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
...
@@ -588,7 +694,7 @@ def test_only_mash_empty_lstinfo(capsys):
...
@@ -588,7 +694,7 @@ def test_only_mash_empty_lstinfo(capsys):
verbose
=
1
verbose
=
1
quiet
=
False
quiet
=
False
with
pytest
.
raises
(
SystemExit
):
with
pytest
.
raises
(
SystemExit
):
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
verbose
,
quiet
)
...
@@ -615,6 +721,7 @@ def test_only_mash_no_lstinfo(capsys):
...
@@ -615,6 +721,7 @@ def test_only_mash_no_lstinfo(capsys):
NCBI_species_name
=
""
NCBI_species_name
=
""
NCBI_species_taxid
=
""
NCBI_species_taxid
=
""
NCBI_taxid
=
""
NCBI_taxid
=
""
NCBI_strains
=
""
NCBI_section
=
"
refseq
"
NCBI_section
=
"
refseq
"
levels
=
""
levels
=
""
outdir
=
GENEPATH
outdir
=
GENEPATH
...
@@ -633,7 +740,7 @@ def test_only_mash_no_lstinfo(capsys):
...
@@ -633,7 +740,7 @@ def test_only_mash_no_lstinfo(capsys):
verbose
=
1
verbose
=
1
quiet
=
False
quiet
=
False
with
pytest
.
raises
(
SystemExit
):
with
pytest
.
raises
(
SystemExit
):
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
levels
,
prepare
.
main
(
"
cmd
"
,
NCBI_species_name
,
NCBI_species_taxid
,
NCBI_taxid
,
NCBI_strains
,
levels
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
NCBI_section
,
outdir
,
tmp_dir
,
threads
,
norefseq
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
db_dir
,
only_mash
,
info_file
,
l90
,
nbcont
,
cutn
,
min_dist
,
max_dist
,
verbose
,
quiet
)
verbose
,
quiet
)
...
...
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