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zavolan_group
pipelines
scRNA-seq-simulation
Commits
abb1e512
Commit
abb1e512
authored
3 years ago
by
Melvin Alappat
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feat:logging added
parent
4c591824
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1 merge request
!16
Issue_4
Pipeline
#13898
passed
3 years ago
Stage: qc
Stage: test
Changes
1
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1
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1 changed file
src/primingprob/cli_priming_prob.py
+7
-2
7 additions, 2 deletions
src/primingprob/cli_priming_prob.py
with
7 additions
and
2 deletions
src/primingprob/cli_priming_prob.py
+
7
−
2
View file @
abb1e512
"""
Command-line interface client.
"""
import
argparse
import
logging
import
os
from
pathlib
import
Path
import
sys
from
src.primingprob.priming_prob
import
Probability
as
Pbt
# type: ignore
def
parse_args
():
def
parse_args
():
# Input arguments
"""
Parse CLI arguments.
Returns:
...
...
@@ -47,11 +48,15 @@ def main():
args
=
parse_args
()
if
os
.
path
.
exists
(
args
.
input_file
)
and
os
.
path
.
exists
(
args
.
fasta_file
):
# pragma: no cover
logging
.
basicConfig
(
level
=
logging
.
INFO
,
format
=
'
%(message)s
'
)
logging
.
info
(
"
Starting calculating the priming probabilities...
"
)
paradata
=
Pbt
.
inter_para
(
args
.
input_file
)
Pbt
.
inter_prob
(
paradata
,
args
.
fasta_file
,
args
.
output_file
)
logging
.
info
(
"
Calculations are done...
"
)
logging
.
info
(
f
"
Potential Priming Sites are saved in
{
args
.
output_file
}
"
)
if
not
os
.
path
.
exists
(
args
.
input_file
)
and
os
.
path
.
exists
(
args
.
fasta_file
):
# pragma: no cover
sys
.
exit
(
"
Path to input-file does not exist
"
)
sys
.
exit
(
"
Path to input-file
s
does not exist
"
)
def
init
():
...
...
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