fix: updated cli.py for rewritten class

read_sequencer_package/cli.py

@@ -4,32 +4,34 @@ import logging
 
 parser = argparse.ArgumentParser(prog='read_sequencer',
                                  description='Simulates sequencing of DNA sequences specified by an FASTA file.')
-parser.add_argument('--input_file_path',
+
+parser.add_argument('output',
                     help='path to FASTA file')
-parser.add_argument('--output_file_path',
+parser.add_argument('-i','--input', default=None,
                     help='path to FASTA file')
-parser.add_argument('--read_length',
+parser.add_argument('-r','--read-length', default=100,
                     help='read length for sequencing',
                     type=int)
-parser.add_argument('--random', action='store_true', default=False,
-                    help='generate random sequences')
-parser.add_argument('--n_random', default=100, type=int, help='n random sequences')
-parser.add_argument('--mean_random', default=50, type=int, help='mean random sequences')
-parser.add_argument('--sd_random', default=25, type=int, help='standard deviation random sequences')
+parser.add_argument('-n','--n_random', default=100, type=int,
+                    help='n random sequences. Just used if input fasta file is not specified.')
+parser.add_argument('-s','--chunk-size', default=10000, type=int, help='chunk_size for batch processing')
 
 args = parser.parse_args()
 
 def main():
     LOG.info("Read sequencer started.")
-    read_sequencer = ReadSequencer()
-    if args.random:
-        read_sequencer.add_random_sequences(n=args.n_random, mean=args.mean_random, sd=args.sd_random)
+    if args.input is not None:
+        read_sequencer = ReadSequencer(fasta=args.input, output=args.output, read_length=args.read_length, chunk_size=args.chunk_size)
+        read_sequencer.get_n_sequences()
     else:
-        read_sequencer.read_fasta(args.input_file_path)
-    read_sequencer.run_sequencing(args.read_length)
-    read_sequencer.write_fasta(args.output_file_path)
+        read_sequencer = ReadSequencer(fasta=args.input, output=args.output, read_length=args.read_length, chunk_size=args.chunk_size)
+        read_sequencer.define_random_sequences(n=args.n_random)
+
+    read_sequencer.run_sequencing()
+
     LOG.info("Read sequencer finished.")
 
+
 if __name__ == '__main__':
     logging.basicConfig(
         format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',

read_sequencer_package/read_sequencer.py

@@ -36,7 +36,6 @@ class ReadSequencer:
                  None
         """
         self.n_sequences = len(list(SeqIO.parse(self.fasta, 'fasta')))
-        LOG.info(self.n_sequences, ' sequences found in ', self.fasta)
 
     def define_random_sequences(self, n: int) -> None:
         """
@@ -48,8 +47,6 @@ class ReadSequencer:
             Returns:
                 None
         """
-        LOG.info('Set mode to: generate random sequences')
-        LOG.info('N random sequences: ', n)
         self.random = True
         self.n_sequences = n