Skip to content
Snippets Groups Projects
Commit 0303732b authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Limit sequence format to fasta or genbank

parent 99ca7382
No related branches found
No related tags found
2 merge requests!2PyPI publish package,!1Package this lib for pypi
Pipeline #18280 passed
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"
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment