From 0303732b849a14554d24ec16b484f39e5780f442 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 15 Nov 2019 12:50:26 +0100
Subject: [PATCH] Limit sequence format to fasta or genbank
---
crisprbact/cli.py | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
diff --git a/crisprbact/cli.py b/crisprbact/cli.py
index a3cc12f..081278d 100644
--- a/crisprbact/cli.py
+++ b/crisprbact/cli.py
@@ -1,6 +1,6 @@
-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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