deleted: ../dist/read_sequencer-0.0.0-py3-none-any.whl

	deleted:    ../dist/read_sequencer-0.0.0.tar.gz
	deleted:    ../dist/read_sequencer-0.1.0-py3-none-any.whl
	deleted:    ../dist/read_sequencer-0.1.0.tar.gz
	modified:   ../read_sequencer.egg-info/PKG-INFO
	modified:   cli.py
	modified:   modules.py
	modified:   ../setup.py
	../build/
	../dist/

read_sequencer.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: read-sequencer
-Version: 0.1.0
+Version: 0.1.1
 Summary: Simulates sequencing with a specified read length from sequences specified by a FASTA file.
 Home-page: https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer
 Author: Clara Serger, Michael Sandholzer and Christoph Harmel

read_sequencer_package/cli.py

 import argparse
 from modules import read_sequencer as rs
+import logging
 
 parser = argparse.ArgumentParser(prog='read_sequencer',
                                  description='Simulates sequencing of DNA sequences specified by an FASTA file.')
@@ -14,10 +15,17 @@ parser.add_argument('--read_length',
 args = parser.parse_args()
 
 def main():
+    LOG.info("Program started.")
     read_sequencer = rs()
     read_sequencer.read_fasta(args.input_file_path)
     read_sequencer.run_sequencing(args.read_length)
     read_sequencer.write_fasta(args.output_file_path)
+    LOG.info("Program finished.")
 
 if __name__ == '__main__':
+    logging.basicConfig(
+        format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+        level=logging.INFO,
+    )
+    LOG = logging.getLogger(__name__)
     main()

read_sequencer_package/modules.py

+import logging
+LOG = logging.getLogger(__name__)
+
 def generate_sequences(n, mean, sd):
     """
     Generates random sequences.
@@ -11,6 +14,7 @@ def generate_sequences(n, mean, sd):
         list: of n sequences
     """
     from random import gauss, choice
+    LOG.info("Generating sequences.")
     dict = {}
     for i in range(n):
         keys = range(n)
@@ -33,6 +37,7 @@ def read_in_fasta(file_path):
         Dict: It returns a dictionary with sequences.
 
     '''
+    LOG.info("Reading in FASTA files from destination.")
     sequences = {}
     f = open(file_path)
     for line in f:
@@ -59,6 +64,7 @@ def read_sequence(seq, read_length):
         str: returns sequenced element
 
     '''
+    LOG.info("Reading sequences.")
     from random import choice
     bases = ["A", "T", "C", "G"]
     sequenced = ''
@@ -84,6 +90,7 @@ def simulate_sequencing(sequences, read_length):
     Returns:
         dict: of n sequences as values 
     """
+    LOG.info("Sequencing in progress....")
     results = {}
     for index, key in enumerate(sequences):
         results[key] = read_sequence(sequences[key], read_length=read_length)
@@ -103,6 +110,7 @@ def generate_sequences(n, mean, sd):
     Returns:
         dict: of n sequences
     """
+    LOG.info("Generating random sequences.")
     dict1 = {}
     for i in range(n):
         keys = range(n)
@@ -123,13 +131,14 @@ def write_fasta(sequences, file_path):
         file_path (str): A file path directing to the output folder.
         
     """
+    LOG.info("Writing FASTA file.")
     from textwrap import wrap
     with open(file_path, "w") as outfile:
         for key, value in sequences.items():
             outfile.write(key + "\n")
             outfile.write("\n".join(wrap(value, 60)))
             outfile.write("\n")
-
+    LOG.info("Sequencing was successfully executed.")
 class read_sequencer:
     def __init__(self):
         self.sequences = {}

setup.py

@@ -2,13 +2,13 @@ from setuptools import setup, find_packages
 
 setup(
     name='read_sequencer',
-    version='0.1.0',
+    version='0.1.1',
     url='https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer',
     license='MIT',
     author='Clara Serger, Michael Sandholzer and Christoph Harmel',
     author_email='christoph.harmel@unibas.ch',
     description='Simulates sequencing with a specified read length from sequences specified by a FASTA file.',
     packages=find_packages(),
-    install_requires=['random','textwrap','argparse'],
+    install_requires=['random','textwrap','argparse','logging'],
     entry_points={'console_scripts': ['read_sequencer=read_sequencer_package.cli:main']}
 )