From e6d23812675b230dcf821e6a7a09d08ae4c5f746 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Wed, 26 Feb 2020 11:33:58 +0100
Subject: [PATCH] Change command option name
---
crisprbact/cli.py | 59 +++++++++++++++++++++++++++++++++--------------
1 file changed, 42 insertions(+), 17 deletions(-)
diff --git a/crisprbact/cli.py b/crisprbact/cli.py
index 3b30605..8f7552f 100644
--- a/crisprbact/cli.py
+++ b/crisprbact/cli.py
@@ -52,19 +52,28 @@ def predict(config):
@predict.command()
-@click.option("-t", "--target", type=str, required=True)
-@click.option("-g", "--genome", type=click.File("rU"), help="Genome")
@click.option(
- "-gf",
- "--genome-format",
+ "-t", "--target", type=str, required=True, help="Sequence file to target",
+)
+@click.option(
+ "-s",
+ "--off-target-sequence",
+ type=click.File("rU"),
+ help="Sequence in which you want to find off-targets",
+)
+@click.option(
+ "-w",
+ "--off-target-sequence-format",
type=click.Choice(["fasta", "gb", "genbank"]),
default=GENOME_FORMAT,
show_default=True,
- help="Genome Format",
+ help="Sequence in which you want to find off-targets format",
)
@click.argument("output-file", type=click.File("w"), default="-")
@pass_config
-def from_str(config, target, genome, genome_format, output_file):
+def from_str(
+ config, target, off_target_sequence, off_target_sequence_format, output_file
+):
"""
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
activity from a target gene.
@@ -74,8 +83,8 @@ def from_str(config, target, genome, genome_format, output_file):
"""
if config.verbose:
print_parameters(target)
- if genome:
- genome_fh = SeqIO.parse(genome, genome_format)
+ if off_target_sequence:
+ genome_fh = SeqIO.parse(off_target_sequence, off_target_sequence_format)
else:
genome_fh = None
guide_rnas = on_target_predict(target, genome_fh)
@@ -86,31 +95,47 @@ def from_str(config, target, genome, genome_format, output_file):
@predict.command()
@click.option(
- "-t", "--target", type=click.File("rU"), required=True, help="Sequence file",
+ "-t",
+ "--target",
+ type=click.File("rU"),
+ required=True,
+ help="Sequence file to target",
)
@click.option(
"-f",
"--seq-format",
type=click.Choice(["fasta", "gb", "genbank"]),
- help="Sequence file format",
+ help="Sequence file to target format",
default="fasta",
show_default=True,
)
# @click.option(
# "-s", "--seed-size", type=click.IntRange(8, 15, clamp=True),
# )
-@click.option("-g", "--genome", type=click.File("rU"), help="Genome")
@click.option(
- "-gf",
- "--genome-format",
+ "-s",
+ "--off-target-sequence",
+ type=click.File("rU"),
+ help="Sequence in which you want to find off-targets",
+)
+@click.option(
+ "-w",
+ "--off-target-sequence-format",
type=click.Choice(["fasta", "gb", "genbank"]),
default=GENOME_FORMAT,
show_default=True,
- help="Genome Format",
+ help="Sequence in which you want to find off-targets format",
)
@click.argument("output-file", type=click.File("w"), default="-")
@pass_config
-def from_seq(config, target, seq_format, genome, genome_format, output_file):
+def from_seq(
+ config,
+ target,
+ seq_format,
+ off_target_sequence,
+ off_target_sequence_format,
+ output_file,
+):
"""
Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
activity from a target gene.
@@ -125,8 +150,8 @@ def from_seq(config, target, seq_format, genome, genome_format, output_file):
for record in SeqIO.parse(target, seq_format):
if config.verbose:
click.secho(" - search guide RNAs for %s " % record.id, fg=fg)
- if genome:
- genome_fh = SeqIO.parse(genome, genome_format)
+ if off_target_sequence:
+ genome_fh = SeqIO.parse(off_target_sequence, off_target_sequence_format)
else:
genome_fh = None
guide_rnas = on_target_predict(str(record.seq), genome_fh)
--
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