From a15b96e70b8173c63092efccdcd5227d23dc5800 Mon Sep 17 00:00:00 2001
From: Eric Boittier <ericdavid.boittier@unibas.ch>
Date: Mon, 12 Dec 2022 16:09:49 +0100
Subject: [PATCH] testing CI
---
.gitlab-ci.yml | 4 ++--
cdna/cdna.py | 4 ++--
cdna/cli.py | 21 ++++++++++++++++-----
3 files changed, 20 insertions(+), 9 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 09a5677..5adc43e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,5 +6,5 @@ default:
my_tests:
# Good to put a small description here of what this job does
script:
- - echo "Command 1"
- - echo "Command 2"
+ - black cdna
+ - pylint cdna
diff --git a/cdna/cdna.py b/cdna/cdna.py
index c5f6d31..326d905 100644
--- a/cdna/cdna.py
+++ b/cdna/cdna.py
@@ -140,7 +140,7 @@ class CDNAGen:
self.fasta_dict = {x.name: x for x in records}
def read_csv(self) -> None:
- """ Reads a given copy number csv file
+ """Reads a given copy number csv file
Wrapper for Pandas read_csv.
@@ -185,7 +185,7 @@ class CDNAGen:
id_CSV = str(row["seqname"]).split("_")[1]
# Calculate Normalized_Binding_Probability and add to GTF dataframe
df_input_GTF.loc[index, "Normalized_Binding_Probability"] = (
- row["Binding_Probability"] / df_normalization_bind_probablility[id_GTF]
+ row["Binding_Probability"] / df_normalization_bind_probablility[id_GTF]
)
# Calculate Normalized_Binding_Probability and add to GTF dataframe
csv_transcript_copy_number = self.df_input_CSV.loc[
diff --git a/cdna/cli.py b/cdna/cli.py
index f3100e0..e8e2cd7 100644
--- a/cdna/cli.py
+++ b/cdna/cli.py
@@ -9,14 +9,25 @@ def parser():
prog="cDNA generator",
description="Generate cDNA sequences based on primer probabilities.",
)
- parser.add_argument("-ifa", "--input_fasta", help="genome fasta file", required=True)
+ parser.add_argument(
+ "-ifa", "--input_fasta", help="genome fasta file", required=True
+ )
parser.add_argument("-igtf", "--input_gtf", help="gtf file", required=True)
- parser.add_argument("-ofa", "--output_fasta", help="output fasta file", required=True)
- parser.add_argument("-icpn", "--input_copy_number", help="input copy number (csv) file", required=True)
- parser.add_argument("-ocsv", "--output_csv", help="output fasta file", required=True)
+ parser.add_argument(
+ "-ofa", "--output_fasta", help="output fasta file", required=True
+ )
+ parser.add_argument(
+ "-icpn",
+ "--input_copy_number",
+ help="input copy number (csv) file",
+ required=True,
+ )
+ parser.add_argument(
+ "-ocsv", "--output_csv", help="output fasta file", required=True
+ )
args = parser.parse_args()
- print(' \n'.join(f'{k}={v}' for k, v in vars(args).items()))
+ print(" \n".join(f"{k}={v}" for k, v in vars(args).items()))
print()
CDNA = CDNAGen(
ifasta=args.input_fasta,
--
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