From 3f8464a3e87a41925ad54ff50771eafee2c16273 Mon Sep 17 00:00:00 2001
From: Christoph Harmel <christoph.harmel@unibas.ch>
Date: Tue, 20 Dec 2022 13:11:29 +0100
Subject: [PATCH] fix: small edits
---
.gitignore | 3 ++-
Dockerfile | 2 +-
README.md | 33 ++++++++++++++++++++++++++++-----
readsequencer/cli.py | 2 +-
4 files changed, 32 insertions(+), 8 deletions(-)
diff --git a/.gitignore b/.gitignore
index 42770ec..83c7b50 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
.DS_Store
.idea/
-
+read_sequencer.egg-info
+readsequencer.egg-info
# Created by https://www.toptal.com/developers/gitignore/api/python
# Edit at https://www.toptal.com/developers/gitignore?templates=python
diff --git a/Dockerfile b/Dockerfile
index eb44f01..f2b74d7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
FROM python:3.11.1-slim-bullseye
# MAINTAINER add_maintainer
-
+MAINTAINER "Christoph Harmel"
# set names for user, group and user home
ARG USER="bioc"
ARG GROUP="bioc"
diff --git a/README.md b/README.md
index 3003dfb..4895b87 100644
--- a/README.md
+++ b/README.md
@@ -2,25 +2,48 @@
## Overview
-Read Sequencer is a test python package to simulate sequencing.
+Read Sequencer is a python package to simulate sequencing.
It reads fasta files, simulate sequencing with specified read length and writes the resulting sequences into a new fasta file.
-## Installation from PyPI
+## Installation from github
Read Sequencer requires Python 3.9 or later.
-Install Read Sequencer from PyPI using:
+Install Read Sequencer from Github using:
```
-pip install -i https://test.pypi.org/simple/ read-sequencer==0.1.1
+git clone https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer.git
+cd read-sequencer
+pip install .
```
## Usage
```
-read_sequencer --input_file_path --output_file_path --read_length
+usage: read_sequencer [-h] [-i INPUT] [-r READ_LENGTH] [-n N_RANDOM] [-s CHUNK_SIZE] output
+Simulates sequencing of DNA sequences specified by an FASTA file.
+
+positional arguments:
+ output path to FASTA file
+
+optional arguments:
+ -h, --help show this help message and exit
+ -i INPUT, --input INPUT
+ path to FASTA file
+ -r READ_LENGTH, --read-length READ_LENGTH
+ read length for sequencing
+ -n N_RANDOM, --n_random N_RANDOM
+ n random sequences. Just used if input fasta file is not specified.
+ -s CHUNK_SIZE, --chunk-size CHUNK_SIZE
+ chunk_size for batch processing
+
```
+
+## Docker
+
+The docker image is available on docker hub: https://hub.docker.com/r/grrchrr/readsequencer
+
## Contributors and Contact Information
Christoph Harmel - christoph.harmel@unibas.ch
diff --git a/readsequencer/cli.py b/readsequencer/cli.py
index 76afc5a..cc74c44 100644
--- a/readsequencer/cli.py
+++ b/readsequencer/cli.py
@@ -7,7 +7,7 @@ LOG = logging.getLogger(__name__)
def main():
parser = argparse.ArgumentParser(
- prog="read_sequencer",
+ prog="readsequencer",
description="Simulates sequencing of DNA sequences specified by an FASTA file.",
)
--
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