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David BIKARD
CRISPRbact
Commits
0303732b
Commit
0303732b
authored
5 years ago
by
Remi PLANEL
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Limit sequence format to fasta or genbank
parent
99ca7382
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2 merge requests
!2
PyPI publish package
,
!1
Package this lib for pypi
Pipeline
#18280
passed
5 years ago
Stage: test
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crisprbact/cli.py
+13
-4
13 additions, 4 deletions
crisprbact/cli.py
with
13 additions
and
4 deletions
crisprbact/cli.py
+
13
−
4
View file @
0303732b
import
click
from
crisprbact
import
on_target_predict
from
Bio
import
SeqIO
import
click
class
Config
(
object
):
...
...
@@ -32,7 +32,8 @@ def predict(config):
@pass_config
def
from_str
(
config
,
target
,
output_file
):
"""
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
activity from a target gene.
[OUTPUT_FILE] file where the precitions are saved. Default =
"
stdout
"
...
...
@@ -49,12 +50,20 @@ def from_str(config, target, output_file):
@click.option
(
"
-t
"
,
"
--target
"
,
type
=
click
.
File
(
"
rU
"
),
required
=
True
,
help
=
"
Sequence file
"
)
@click.option
(
"
-f
"
,
"
--seq-format
"
,
help
=
"
Sequence file format
"
,
default
=
"
fasta
"
)
@click.option
(
"
-f
"
,
"
--seq-format
"
,
type
=
click
.
Choice
([
"
fasta
"
,
"
fa
"
,
"
gb
"
,
"
genbank
"
]),
help
=
"
Sequence file format
"
,
default
=
"
fasta
"
,
show_default
=
True
,
)
@click.argument
(
"
output-file
"
,
type
=
click
.
File
(
"
w
"
),
default
=
"
-
"
)
@pass_config
def
from_seq
(
config
,
target
,
seq_format
,
output_file
):
"""
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
activity from a target gene.
[OUTPUT_FILE] file where the precitions are saved. Default =
"
stdout
"
...
...
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