Merge branch 'build_docker' into 'main'

fix: small edits

See merge request !36

.gitignore

 .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
 

Dockerfile

 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"

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  

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.",
     )