feat: added random sequence generator to cli

read_sequencer_package/cli.py

 import argparse
-from modules import read_sequencer as rs
+from modules import ReadSequencer
 import logging
 
 parser = argparse.ArgumentParser(prog='read_sequencer',
@@ -11,21 +11,28 @@ parser.add_argument('--output_file_path',
 parser.add_argument('--read_length',
                     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')
 
 args = parser.parse_args()
 
 def main():
-    LOG.info("Program started.")
-    read_sequencer = rs()
-    read_sequencer.read_fasta(args.input_file_path)
+    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)
+    else:
+        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.")
+    LOG.info("Read sequencer finished.")
 
 if __name__ == '__main__':
     logging.basicConfig(
         format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
-        level=logging.INFO,
-    )
+        level=logging.INFO)
     LOG = logging.getLogger(__name__)
     main()

read_sequencer_package/fasta_testfile/result.fasta

 1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 481 bp
-tgagcactcggtgccaagggcggggatacacagatggttggctgatacaaccgggactta
-aattccctagactagatctgtgttggaacgcctctctacgagaaggcgaacgaactggcg
-ccgaggcgatcgctaacatcttcgtctcgcttgaaccacacaatggatgattcctcccta
-ggggtttgacaatcaacctggatagcgtttaatatagatggctggttgatttgtaaggcc
-ttcacagactactcagagcaataagtgaccccccaacaatcagaggctgatcctctgctc
+tgagcactcggtgccaagggcggggatacacagatggttggctgatacaa
 2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 495 bp
-ctgaatcaggtgtaggttctttttacgtcgtttaaggagctacacggtatcttgttttca
-gttaaggtgccacacccccgggtggatcatccgtcagctttcctacaattaggtaactgg
-cgggatcatttagtcttgtattaagacgctcgcgcccggggcggccggcttgtttgtgga
-gagaaacaacaagtctgagtatagattaaatacaactggtttactggcaagtcagcgcgt
-aacaaccggtgagccgctgcgcatgcttactgcaatgaacatcttggcacgatcctgcga
+ctgaatcaggtgtaggttctttttacgtcgtttaaggagctacacggtat
 3|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 193 bp
-acttcagtactggaaggatctaggaaccattaatgcgagtgtggtgacgccagacgaccc
-ccggtgttctgccaccttctttggataggagaaccgtcactcgccccggaggccccacgg
-ataagaagggtatcttgtgatcacgcgaatgactcacttgcgtaagtaatctaactttgt
-ttttcgctataaaAAGCCGGGGTGTTGAAGTCTATCGTCGATGGCTGCAGTATTAAAGAT
-CTTATGACTAATGCTCCAGCTTCCCCTCTGTGGTTAGAGACGAACTCGTCAGCCTCGATT
+acttcagtactggaaggatctaggaaccattaatgcgagtgtggtgacgc
 4|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 625 bp
-acgtctggagcgtgggttgacccctgtacatggttctttccggatccttaacgtgccgat
-acaactcaaaggtaactgtgcttaccacttccgaagctacatgcctctaacaaagtactt
-tcgaggaggcactcaacccccggagatgctttgcgcggaagcagagatcgctgctcaaaa
-tttggaatcactttcgtgcgagacccaaacaatttatggtggattcaagcgaacgagtca
-tgattacagatctatcaatcgaggagaggacggcttcgccgtttccttttaatgtgaaac
+acgtctggagcgtgggttgacccctgtacatggttctttccggatcctta
 5|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 845 bp
-agagcgtacggcgcgcatcgtataccctacgagggcggcgtgtggaggaacgctgggctg
-acactgtagaagattagatacacttgtccctaaaattaacccttaaccgctattagccgt
-gaacgcttcctaatatttcaagccgtatagctaagtggagaatgtggagccctggtcaaa
-tcacgagccaattagccctagacggacagcacatctcgtcgcgttaagcggaacactcag
-cttttattacctagtgctcagcctggtttccatatgctctaaccgaactgatgcatactt
+agagcgtacggcgcgcatcgtataccctacgagggcggcgtgtggaggaa
 6|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 703 bp
-tgcagtcgatgtgctattcgttttaggcagtctacgcgcttagtaactcccacggccata
-gacttatctcagacatggaccatgtcgatatcggacgccgtcttaccacatttttcatag
-cccttcataaggcagcgtgctcttactgcccaataaggtggacgattccgaccctaggcg
-aaccagcgctatagatggaccttctaattgatgcgcaacgtgattgtttccttggtctgg
-gttagcatttcggtagcctaacagtcactccagttcgctaactggcctggatgagggccc
+tgcagtcgatgtgctattcgttttaggcagtctacgcgcttagtaactcc
 7|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 243 bp
-actctttagaatgggtttcactaatagtacgtgcatacaatttcgtcagaaagggcgctt
-gctaagggacacggatcaatgatgaccagacttatggtgtcaggtctcactatattacat
-atccggaacccgtgcccgcaccacgcgctgggtctaggcgaccggtgcatcatctccgcg
-tctctagaggattctctcggtaaatgctgaattgcgtgagatcaaatccgtatgccagtc
-atgAGGCAAGGCGTATAGATCTTTCCTCAGCATGAACCGGAACATCCTACAATCGCACGC
+actctttagaatgggtttcactaatagtacgtgcatacaatttcgtcaga
 8|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 863 bp
-attggcccggtccaggacagagccttatattgctactggtatgagaaccgttctgacgta
-aacttgatggctttacgcctgcacgggcttcatacacacatgaccgtggacaaagtcgcc
-caggccctcgaatagggtgtaatggttaacggttagtgccaccccaatgggtgcgaggca
-gtaagagtgtcctatggcaaaactctcctcgtttcagaagggtcgctcctctagcctcct
-tatcccccctataatagtactcgccgggtacgagccggagctccctcgagaagtcatcct
+attggcccggtccaggacagagccttatattgctactggtatgagaaccg
 9|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 494 bp
-aagcgaaactcctagaacttcccatcaggcaatcgtgtcccacgaagcacggatactacg
-ggcactagttgaatggggggtttttttcgtaggtcgtaataggtactcggatagtcggcc
-cagagttatgcttaagaatgcgctgcttaattcaatgtgactgccgttgtctccgatcag
-atccaggtgatgattgcgatcgcagcgacatatgtctcgaaagacgtgtcgtgaataagc
-ctgtaagcccaatgcaacatggttccctcaccttgtagctgatgtaccgtgtttcaatct
+aagcgaaactcctagaacttcccatcaggcaatcgtgtcccacgaagcac
 10|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 86 bp
-atcctagcgccaaagatttactgttatggggtcgacgaacactagccgataatgccgtcc
-tgggatctctagcctagtattatgcgGACGTTTCCAGCCCCGCTGACCCTGAGTCGGACG
-TGAAAGCGAATCATCATATAAAGCATACACTGACTTGCACAAGTTGAAATAAGAGGTTCG
-CTTAGGCTTGCCTCTCTAGTGGCGCAGCAGTACTGAGTGGGTTCTACTTACTCTCTGGAC
-TCATGATCGTGTACACCGTGAAAGACGGCCCATGTGCCGTATATCTACCGTGCATAACCT
+atcctagcgccaaagatttactgttatggggtcgacgaacactagccgat
 11|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 360 bp
-cgcctgagggtcctaaatctgacgtatgatcgaagagattggaaggtcccggcgggtcac
-cccacgttgcgatcatggccaaggccatggtttgctcaaaaatcccacattcgccgtctt
-acgcgttaggacctcactatcccacagacggtgcgttaccttgtagttgacgcgggatcg
-tggtgataacagctatttccgagacttcatattcttttacatagcggcttaccgtagtga
-ctccatacattatttgcctattttgtagtgccccgaacagtaaggggaagccaactgccg
+cgcctgagggtcctaaatctgacgtatgatcgaagagattggaaggtccc
 12|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 140 bp
-gaattcctggggatttactcacccccgaggcggacaagatttccagctggatcaccgagg
-gttacttaatcccttcgatgctttcaaaggccctaatcagtattgagcaacgaaagcgga
-gtcgttagtgtccaagttgcAAATGGTATCGCAGAGCGGTCGGATTCGCCAAAAAGCTTG
-GCCAATGGCTAAAATTTAGCTCTCGCCCTCGCGGACATTGTGGACATGTGCCTGACTACC
-CATCATTCTCGCTCGGCACTAGGCCACCAGGGTTAACGATTTCGTAACAACGACCCGCAT
+gaattcctggggatttactcacccccgaggcggacaagatttccagctgg
 13|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 832 bp
-aatactctcgttgaagcgtcggacagtaaagtgagagatttcggcccacggtagtcggac
-attctcagtggggagcgaagagttgcgcttagagccgacgtacacgatataacctcaatt
-gaaaatcgctatgtgcatcgttagggcctccggcgtgctgtttcggcagctgagtgtgag
-ggtataacttaccttcgacccgaattgtctcgcggaaatcctaggcaagtaatccacttt
-tggtacgggggagctagttcctctaagacgaacaagtgcactcttcacgtatagtgccct
+aatactctcgttgaagcgtcggacagtaaagtgagagatttcggcccacg
 14|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 296 bp
-atcggggtgcgaaatcccctgagctggttgactacatacgtaaccacgttccgtgcgtca
-tctaagcgtatcggctcatactggtggtaactagacttggtgaaccctaggtgccggcat
-atcgaggtccgcatccaaaataactatcgctatagctacatagacatttactcgcaatat
-tacacgaaccgtacgtccctcggtattaacgtaatggttaaagtctctaattccgctgca
-gagcggcgggataaagacgccggtgtggcctgaatggtggatctgtccgtagtaccACGT
+atcggggtgcgaaatcccctgagctggttgactacatacgtaaccacgtt
 15|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 515 bp
-accttcaatttgttcgcccgggacaagtagaaattactgtaaactaaacttaacctattc
-cttgttaaagtccgcaccaagtgtactgtaagaatggtcgctcgtaataataacgagaag
-atcctcgagccgtggtctgctgcaactaccttgagcggtacatcgatgtcccactctggg
-cggggatcaggggcgagacttgtggtgaggccaaagaatggcgcatatgtaggcaccata
-cgtcgatacgttccaggagtagaggcctcgaacatacaccacgataagtctacagacgca
+accttcaatttgttcgcccgggacaagtagaaattactgtaaactaaact
 16|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 820 bp
-ccggctcaatcctgtagaaccgcgtacaacacacccaagctataccgcacacggcgcctt
-agcaaccactgcttatctgcgtattatacctttacaatcattacatttgatctatctgtg
-taccggttttttttgattcaattcgctggattacgacctcccggccaaaaattctcaatt
-catcgttaacagacgtatttgaagataatcattcaacgtgaactagcacttggtcacttg
-gtacgccaaccaagctgtgctttggggcaaccctttataactcacatgccgtcctaggac
+ccggctcaatcctgtagaaccgcgtacaacacacccaagctataccgcac
 17|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 791 bp
-attgttagggcctgtccggaaaagatcaacggaagatattcaccagcacctatgctgact
-cacgtagttcccgacgttcagtcccctccaacgtggaaggtaggacccatctccttaacg
-ggatcgatcggtcttcctgtgaaagttgctcagagtcctcaaggacgtttttgggtgcgt
-gtacggtatggttatggtacgtgtctgtgacagagggtattcttactggttaagtgaccc
-atatgaccacctgacgcccgagcatagacctgtaggggtcgacgcgagagatggcagctt
+attgttagggcctgtccggaaaagatcaacggaagatattcaccagcacc
 18|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 328 bp
-accgattacaggcagtcggccttgtccgctcgtatatccagggatgttccaccgaaagtg
-ggagtgtggcacttattggtaaaaggcatttttacgaacgacactgataggattgatcac
-tcaagaaatgttctcgaccctgaggtaggagtcttaacagacggacatcctccgtagata
-cgtgagaattaagggacgcatgtcgaaaacgcttggaatctactgtagtggcccacctta
-cgcttcttccaataactcccttcatagtccggcaacctcggtgggggtttcccttaggcc
+accgattacaggcagtcggccttgtccgctcgtatatccagggatgttcc
 19|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
-ggagtggaaaattctgtagtccgttggcggcgaccgcaaaccagaataatatggtcacgt
-taggccctcgggccccttcatatgtacggagtcattgaattagcattatactaccgttac
-gcaagaccctatcccatccgcgactgtcaccactgctgtaaggttgcaaggctgtttcaa
-tgtaaagtaggcgaattctgacgtgggctgataacgaatcccccgggttatctagtgcaa
-gtgctatccCAGCAGTAGCTGTTGACTCGGAGGCGTCAGAACTTCCCTCTAGTGTGGCAA
+ggagtggaaaattctgtagtccgttggcggcgaccgcaaaccagaataat
 20|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 440 bp
-atcttaaacagcccaatcggctcgccgaccaatttcccgcttcacagtacgcggaagaat
-ctgcagatagaagtcagccctctcacgtcaataggaatgctgcccgtcatgtttaactac
-tcaagttttaaggtgtcccttatcggttccaggatcatgtctgaaggaagatggtcgcaa
-cgaaatctggagtggcatacatcgttcggtcgaagcataatctcagacgttatctataaa
-gttagggcgctgtatggattgggattcaagctcgaagcctgttcctgccatacagcgcct
+atcttaaacagcccaatcggctcgccgaccaatttcccgcttcacagtac
 21|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 840 bp
-cataactcgtgagtggccctgtacaagtcattgcatcacaatccttgcaatttgctcctt
-tggccaagcgtacaagaccccggacccatacgctcccggctgataaactgctacagcatg
-gtatatccggatgatgcccctgaaaactgcggaagtcaatttgttgatgaatccccgact
-ttccgctgttcctgtggatggtcgaatgccaaatgaagagctgctccccccttctttaat
-atcaagcactacaaagataaagcctgtttggctgacggcgagccctcccctatcgtacgc
+cataactcgtgagtggccctgtacaagtcattgcatcacaatccttgcaa
 22|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 234 bp
-caccgcgaaagtgactcagttttcccggtcttatcacggtcgttgtcgtccagattccgg
-ttgttaactgcgggagctataacacttattccttactgcgacggctgatccactaagaac
-agttcatagagctcggctatataatttgaagacatagattccacggtacttgtagcccat
-aaccgctgaggaggaacgtccaacggttcgcgcggagcatgtgacgcttaaaggGATGTA
-AACAAAAGTTTCCAGGCGGCGGCGGTGTAGGCCGTTGCACTGTACTAGGCACAGCTACTG
+caccgcgaaagtgactcagttttcccggtcttatcacggtcgttgtcgtc
 23|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 917 bp
-atcaagtgattacctggtaacccgccgctcttgcagtgttcaccctttgtgtcgtcttag
-tgtttgtacacgttaaggaaaagcgttagcttaaccattacgccccccaaagcccggtgt
-gtagttatctacatgccgtgtcaaagcggtgactaaatgtttatcaagttctgatgacaa
-cgtgagctcttaaagccattgactagtataagcacggaacaatgataccaggcaagcttg
-aatataggataaggcctctaagctcgaagcggatcttacggaggtgtgaatcaacagcac
+atcaagtgattacctggtaacccgccgctcttgcagtgttcaccctttgt
 24|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 676 bp
-cacacggcatcgcaaagcgagctatccagagatgatacatgtggttgaaggtgattgcgt
-caacatgggggttgctcagtttggttggtcaatcaacggtggcagaccatgcgataacga
-tgatggtaagactgtaaggtaagttaaatactctcgtctgccagttgggtcgtcaacgct
-gcagagacgccattcttcccagaaggtccgagctttctacagtgccgcggcgtcatgacc
-aaaggggtccaacctcgcagtaaaatgtctatgcttctggtttggaatgagaccgggcca
+cacacggcatcgcaaagcgagctatccagagatgatacatgtggttgaag
 25|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 870 bp
-ctgatcaccaatagcttgcgcttaacacacgcgccttacaattatatgacgcccttgcca
-atgacagatagagccattaatcgtggaaaccaggcatttatacttgtccgatgtatcgat
-tctcctctatctacagagcccggacatgcgaaatatcaaaattccatgtatactgaataa
-atacattgggcaagccgggctcatgcagcaatcccagcgttgccttacgcaaagatatct
-tacggagttgcctttagattaacagcacgtgttcaaaaacctagccaactctgtcggtct
+ctgatcaccaatagcttgcgcttaacacacgcgccttacaattatatgac
 26|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 751 bp
-gggtgcgttatggggactaaagactgttactaccggtactccgccttatagagccgtcac
-gtattaatcagctatcaacagatactatcgtcacagccctccttctggcgaaggatctga
-gcatttgcaaagctataagttggtacgcaacggtagagggcttcgtagtcggggaaaggg
-cttgcagtagtataggccgtaacttatctgttgcaacctcaaccgcacgaatcgattact
-ctataactgccctcaatacagtatggttaccagtcaccttcacactgaagattaattcgc
+gggtgcgttatggggactaaagactgttactaccggtactccgccttata
 27|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 574 bp
-gtactgcaccttgcactgctatctacaatgccgagggtcgccctagtgctttgcatgttt
-ggcctctacctacgagtctacgcgggcgtttttaagcaagctacgatcatcttgatccaa
-gggtacgaggccccgcagaccaatggaggtcgtgaccaccctcgtgtatgcctcgcacta
-agcgagcattctggtatactgtctctctcctgtgataataacagtcggctcgatattcag
-ttcacatgaaacagtatgttatataggtgggatggttataacacggaaaggtgaaaaaga
+gtactgcaccttgcactgctatctacaatgccgagggtcgccctagtgct
 28|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 169 bp
-agctccctaaacaacacccgcgtaaaaccttcagttatggtgccgactaaccctgtggat
-gtcttagcgctctcgttccgatgggtgctgatactagtaaatgagactcgagaccgagaa
-cacgcaacggctacaacctggtcggttgttggggtttttataatcagtgTACGAAATAGT
-AGACCTCGCCCTGTAGTTGGAAATTACCGTCATTGGTCTATACAAAGCGCGTGCTTCAGG
-ACTCGGTGCCGAATCACTCCGTGCCAAATTAACGAAAGCTTCTGATGTGGATATGAGTTC
+agctccctaaacaacacccgcgtaaaaccttcagttatggtgccgactaa
 29|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 408 bp
-tgcagtgatgcatcgataagaccgcatagttacctccttacaggtgacgctaggctaatt
-gggagtgctggcacttgtgccctacagtcaagcgctcacgcggtgttctcctcccgcaat
-cttagatattaggctctgtaccgcacgaaggatgaattttcttgactattggtccctgtt
-tacgagggcttacctagagtgaggatgaacataaacaaggcctacttgacttaaggcttc
-caaatcacttgagggcaaatgactcctcaaacgcgagtgccagtactatccgtgagggaa
+tgcagtgatgcatcgataagaccgcatagttacctccttacaggtgacgc
 30|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 52 bp
-caaagcgattcgggttaacgcacttaagagttcgacgtaggttagtcccctcTGAAGCTG
-GCCATAACAGGCAAGTTATTGATTGGACCTTACGACGTACATGGCATTGCGAGACACGGA
-AGCTTGAGCACTCATAGATCTGCCAGTCCCAACGCAAGTTGTTTTTCCCGCATCATTCAG
-AAGAAGAAGACGGATTGAACCAAACTGTCATATCAGTGGTTAGCTGCTGTAAATTCAGCG
-GATTGAGGGATGGGTTTTTCGGAACATTATCTTAGCGGGAACAATAAATGCGAAAACCAG
+caaagcgattcgggttaacgcacttaagagttcgacgtaggttagtcccc
 31|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 581 bp
-tgctctgacgtgtaagcgccttcgataacgtctttgcagcgccccacaaagtaaggaccg
-gtctaacagggcttccgaatcaatagactgatagtaatgggatcctgaggctgggacccg
-acacacggcatattttactagaaacgctgatttaaactccaattatccttgacgcactga
-gccacagtcttagacgcagaatgtccgcaggagccctgtctttcccctaaatcattcgcg
-gcatttgtttacgggttaagtcctgcggatcctagagtctgggccccgtacaaccaggaa
+tgctctgacgtgtaagcgccttcgataacgtctttgcagcgccccacaaa
 32|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
-gcggaactacctctctaagaccgcacaacaagtgtagtagatgaagatcacgcagagtgc
-tcggcactgcatttttatacgtcgaatcagaaacgaggttcctcctctaggcttgttaaa
-aatccgggcgcgatgggctggtaatctgtggccatgggagcctcgccatttaaagatttt
-ggttaaggctcctctgttgtgtccatcacccttgaacgagcccgtacaaaccgtgtacga
-tgttgacacTGCAGAGAGGGCGTTTCGTACCATAACATGCATCCTAGGCGGTCATATTGT
+gcggaactacctctctaagaccgcacaacaagtgtagtagatgaagatca
 33|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 297 bp
-gccctcgcgccagcttacttttagaaaacatcgaccggtaagagatacctgggtgagctg
-ggcttcacgacatgttcttaaatcaatactctaaatctgctttgtagcatgcctcaagta
-aaaaaatgtgctggttccgcacaggtgtgacgattaacgttgcgcccgtttgcgtcagtc
-cagatcaccgatcttccacaccaccggtgggctgccggactgcaggtaatgactcctggc
-tgcattctctgacataaaggttgaatagaacggcgtccttgagaaggttatggaacgAAA
+gccctcgcgccagcttacttttagaaaacatcgaccggtaagagatacct
 34|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 573 bp
-gcctaggggtcttgaccacagggagtacgagcattgatcattggagcaggtggctaatat
-tgatagtggttagaccaccggcgcatcatcgtacgagcgcgggcgatacgtgtctttcac
-cggcgcactaatcttatcttacttctcaagccccgacagcatgtacgccaagtgttgttc
-tgatgaaactttcgaaatagcaactgttagtcagttatagttggggagggcagtgaatac
-ctcaaatacacccaagaaataacttcgaagcggcgcctatatcacacccctgtttcttat
+gcctaggggtcttgaccacagggagtacgagcattgatcattggagcagg
 35|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 559 bp
-gaaaaagtcgccccattcagttacaatcgtcttcagaagccagctcggttggggctatct
-gcggggtaatgcaacagggggctaccagacggtaaaccagggtcttgctattggtgttac
-gaaacaaaggagctatgcgacctcattagatcgagattactctcacaggcagctccggcc
-atagcacaactaatttcgggtgtggagctcaccacaggaacatcttgtgcgtcctttgtt
-atttaattgtgcattgtaatgcaccggaccccgggaacatacagccattatctgtgttgc
+gaaaaagtcgccccattcagttacaatcgtcttcagaagccagctcggtt
 36|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 187 bp
-ctaagtccttatctatgatgcatctttcgttactgcgacaatatccgagacgagcagagt
-tacacgccgaggtgtaaacgaatacgattgctatatgcaacgagttggttacacgcgtga
-aggcgaatgtggatgctgcacttggagtcccattttaccggccgcacgtgctagctcact
-caccttgCAGATATACACAGCTCGGGGCTTATGTGAGGGCTTTCTGTAGATCGGGAGCTT
-ACCAAAATATTATGGCAAGGACTCACACTTTGATATACGCTTCACAATACTAAGTCCAGT
+ctaagtccttatctatgatgcatctttcgttactgcgacaatatccgaga
 37|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 549 bp
-ttcatatggggatttggaatcgggtttgtgcggaatatgcccacgagactgcttatgtca
-acgagacgacccattgtcacgttgtaaggccaccaataacacacaggtcttcgtttgctg
-tctcagggcaatcgcatcgacaacatcgtatggataccgttttttatcagcttacggcgc
-atcatactaataaggtgtttgagagggcgcagactcgaagcagtgtgatcttcccggttc
-gaagatgcaaaaacggtcctatttcgatccaaaactcagcgcactagtccaatgcttttt
+ttcatatggggatttggaatcgggtttgtgcggaatatgcccacgagact
 38|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 916 bp
-gtggcctaccataaatcaatttgggttaacgctctttgatctacgcactatgttgattca
-cttaccccttgtcaccgggcagaagagagccagtttaggtgtggttgtatttgccaaacc
-gcaaaccgcctaatgagctggatccggccatggaattaatcccgtcgtttgactcgaggt
-gttcaaagactgtgcaacacgacgtgcattcatcactagaacttaatctagaccaggcct
-tgtggccaggagaggcgacgtgatattgccctatacacagataattatatacccctcgcg
+gtggcctaccataaatcaatttgggttaacgctctttgatctacgcacta
 39|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 848 bp
-accccggtcgctttggccggtcgtagccctaatcaattctgttcgtatcactaaagtaac
-ggtttgaaatcctttgcaaacttgatctgggtatatgaaccggtatgcggggatagtggt
-aaataagtagtttacgagctgagcgtggattatcccagagaagttgccttaggtccagag
-cccgcacctacaatcactcgaggccggtcgagcgttgcgtggcaaggaaacccagccggt
-caccctaccctcaaactcacgtcattgatccaatcatacatggcgtctctcacggtggtg
+accccggtcgctttggccggtcgtagccctaatcaattctgttcgtatca
 40|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 289 bp
-agagcaaaagaaagtctgctccgcgtgacacacttgctcgttgtagtaactgcacgcgcc
-gtctactcgacagggaccccccgtcggttcctctctatagcaatcgcggaagtggttccc
-tgcctcccgcgcagaagttcaaactagtaatccttaatgacttgtggggggggagatcag
-tttcttccacaatggagtaaacttatgcgagaatcaagatcgcagaggccattttttgat
-gatactgtcagatatgtggttagccgtatcacgttaccgacgcagaattTGGTGAAATAG
+agagcaaaagaaagtctgctccgcgtgacacacttgctcgttgtagtaac
 41|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 642 bp
-ctggggaatgaccgtaccgatctaattccccgtcgaaaaacttatgacgcgcagttgtcc
-ttatgcttgagacatgaatccttgccccatattggcgatcttggccaatgagatctgtcg
-aaagtactggaggccggtaaattgggggctctagaggtccgcccctgaaggactaacgtg
-tgtgtgtgtctacgtgtcgggttatcagcgtgttggacgatggccgtggattcaacgcat
-gctagagagctaatgatcctccgaagtcaaaagcctcagtgcttcgatttatgagcgcgt
+ctggggaatgaccgtaccgatctaattccccgtcgaaaaacttatgacgc
 42|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 993 bp
-gcaagaagccaaaaaccttgcaggaggtcatttaagtttacccgcgcataagcagagacg
-gacctctctgagatctcgcaccgcgcgcccggccggcactatcgatgctagactagggtt
-ggtgactagcccgtcaaaaccagcctaaacgcaaagattgtaggcgctagtccggaactg
-actgcttcgtgtcggtgggagcctagtatgtttccgggtctatgacccctaaaatcatag
-acgtgtcttaatagctatacctgacttactttgaagtacttgccacgacgagtttatgag
+gcaagaagccaaaaaccttgcaggaggtcatttaagtttacccgcgcata
 43|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 473 bp
-ggttgtccaggcgcgagcaagtagctgactcgctaatcttaacgagtattgcttaggact
-tccaaatactccaagacgtcaatacgctttatctttgtgaagtcatcccggaccgagcgc
-ttgggtcgtgatttaaaatcccctgtgatgtggctacaggtgcggcctatacagccgaga
-agaaggccgtctttaggcgtccaatgaaccgttacagggacacaccaaactgcgccaact
-gatcccacgggtcacggtacgctctaagaccagtcgggattctgacttaacatcgcagca
+ggttgtccaggcgcgagcaagtagctgactcgctaatcttaacgagtatt
 44|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 272 bp
-gtagaacttgttccccatggacaatgctagttccgttaatgccaggtattcatgtgccaa
-gcgcctgcctggggaatacgagcctctctacaaacttacggccaccatgcttaaagattc
-ggtgacttcactaatgacctatacaagtaatgcggaggacgctgtcgcttattgctcttt
-gctaaggccagttatgtccgtcagtcaacgatacgctgcggcggtgggtgacggcactag
-accggaagcctgatgacaagttcgaatcaataGTCGCTTCCATTACACTTGCGCTATTCC
+gtagaacttgttccccatggacaatgctagttccgttaatgccaggtatt
 45|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 860 bp
-aaaagcatcactctaacgacgctaccgtctgaatagatcaagattgctatcggttcgacc
-ttgatcgcatgtgaacccgcccaaaaacccgtctcgacaaaagttacgtcgcatgggctg
-cgccaccggatagctcctagcttatcttataaatcaggtagagctacaacatggtgctat
-gacaactggagtgtcatcgctttggcgaaaccgtaaagggtgggaattgctgcattctca
-actgggccgaactattccgcattcggctgctcacaaatcgtggaatgtgtccttgaacgt
+aaaagcatcactctaacgacgctaccgtctgaatagatcaagattgctat
 46|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 884 bp
-aagcctctacaggctctgcggtttggctttacttaacggtgagtcaggaaaacattactg
-ctacgttcaccgtgttcagagatagagagtacattagggaccaatcacaacgttcgccag
-ggcaccgcctaatccgcgttgttagcaagagtacaggctctcgtatactttcagaccctt
-caatactagacgacaaattgcagcccggggtcatcggtcgactcagatacgtgctaacga
-gtaccaggtctaccgttgcaacgttggatgcgttatactcggcataaggcgatgcccttt
+aagcctctacaggctctgcggtttggctttacttaacggtgagtcaggaa
 47|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 888 bp
-gcgccttgaagaggcgaggtctaaaggcaaaaatttagatccgccctatgagacggccga
-cgcggagaattccctaaccactattgtcctctgcatcgatatcaggaataggcttacctg
-caatctcttatggtgatagactgtttgggagctgaacctgagacgcgcacgaaatttgga
-aggatcaaataggccccgcagtctctggtagacttctgccgagcggactagcttggctaa
-ggtgtacaagcctaaatcgtttttcacatcaattttatagctgattatagaggaacgacg
+gcgccttgaagaggcgaggtctaaaggcaaaaatttagatccgccctatg
 48|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 588 bp
-catcaagatgggttacgtaggaccgagattcagtctctgggttagagccgacagcggggc
-cgctacatagtacacggcgaggaatgcggggttgggctgaaccgtacacagtgggctagc
-tgcggtacctgccaccggcatgcgtttaaatcctttcctttggcgaagccaactgccgac
-gtccgcaacagagactcgttttccgaccccgttactaaatcagctaactggcgcctgaat
-cctcttacgtcggatgttaattagtgtatagaatatcggagggttgagtgcgacgcgctt
+catcaagatgggttacgtaggaccgagattcagtctctgggttagagccg
 49|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 626 bp
-taacctcagtctcgttcccccctcggtagttcggacccttattcgcttatctcacattca
-tcactgtagaccaaggaccgggcatacttgcggatatctaccaggactaggcacttaggg
-atacgctgttgaatacgggtttcgtcccgtgtactcaagtgtagtttaagataggtacga
-gtgctagtacatcgtacaatttacaactgacttaaacgagagtttattatgtcttgttca
-cttgttgacacgcctgggaaaataataaaaggcaacgtctaatctcagacccgttgatta
+taacctcagtctcgttcccccctcggtagttcggacccttattcgcttat
 50|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 214 bp
-taactgtcggtcactgctcatcccgactagttcggctcactagacttactcgcggaagcg
-agaagtaggacgtcgtgtaatactccaacgtcgttacgcaatgttgtaaaacttcatcgc
-attccgtgcatggcctaaacgtgcagcattatataacgctctttggtcttaatatccatc
-gcgggagtaacgcgaaggggagacgtgtgcctgaACGAACGCTAAACTAGGTACTAAGTC
-GTGAAGCTCGGGTGGAGACAGGTAAACTGATCGCAACGTATCAACCAATTCTGGACCCTA
+taactgtcggtcactgctcatcccgactagttcggctcactagacttact

read_sequencer_package/modules.py

 import logging
 LOG = logging.getLogger(__name__)
 
-def generate_sequences(n, mean, sd):
-    """
-    Generates random sequences.
-
-    Args:
-        n (int): Amount of sequences to generate.
-        mean (int): mean length of sequence (gaussian distribution).
-        sd (float): standard deviation of length of sequence (gaussian distribution).
-
-    Returns:
-        list: of n sequences
-    """
-    from random import gauss, choice
-    LOG.info("Generating sequences.")
-    dict = {}
-    for i in range(n):
-        keys = range(n)
-        seq = ""
-        nt = ["A", "T", "C", "G"]
-        for value in range(abs(round(gauss(mean, sd)))):
-            seq = seq + choice(nt)
-        dict[keys[i]] = seq
-    return dict
-
-
 def read_in_fasta(file_path):
-    '''
+    """
     This function reads in FASTA files.
 
     Args:
@@ -36,7 +11,7 @@ def read_in_fasta(file_path):
     Returns:
         Dict: It returns a dictionary with sequences.
 
-    '''
+    """
     LOG.info("Reading in FASTA files from destination.")
     sequences = {}
     f = open(file_path)
@@ -52,7 +27,7 @@ def read_in_fasta(file_path):
     return sequences
 
 def read_sequence(seq, read_length):
-    '''
+    """
     This function reads a sequence of a specific read length and adds additional nucleotides if the sequence is 
     smaller then the requested length or cuts the sequence if its longer.
 
@@ -63,12 +38,11 @@ def read_sequence(seq, read_length):
     Returns:
         str: returns sequenced element
 
-    '''
-    
+    """
     from random import choice
     bases = ["A", "T", "C", "G"]
     sequenced = ''
-    if read_length >= len(seq):
+    if read_length > len(seq):
         for nt in range(len(seq)):
             sequenced += seq[nt]
         for nt in range(len(seq), read_length):
@@ -94,10 +68,10 @@ def simulate_sequencing(sequences, read_length):
     results = {}
     for index, key in enumerate(sequences):
         results[key] = read_sequence(sequences[key], read_length=read_length)
-
+    LOG.info("Sequencing was successfully executed.")
     return results
 
-import random
+
 def generate_sequences(n, mean, sd):
     """
     Generates random sequences.
@@ -110,16 +84,17 @@ def generate_sequences(n, mean, sd):
     Returns:
         dict: of n sequences
     """
+    from random import choice, gauss
     LOG.info("Generating random sequences.")
-    dict1 = {}
+    dict = {}
     for i in range(n):
-        keys = range(n)
         seq = ""
         nt = ["A", "T", "C", "G"]
-        for value in range(round(random.gauss(mean, sd))):
-            seq = seq + random.choice(nt)
-        dict1[keys[i]] = seq
-    return dict1
+        for value in range(abs(round(gauss(mean, sd)))):
+            seq = seq + choice(nt)
+        key = str(i) + ': length ' + str(len(seq)) + ' nt'
+        dict[key] = seq
+    return dict
 
 def write_fasta(sequences, file_path):
     """
@@ -138,8 +113,8 @@ def write_fasta(sequences, file_path):
             outfile.write(key + "\n")
             outfile.write("\n".join(wrap(value, 60)))
             outfile.write("\n")
-    LOG.info("Sequencing was successfully executed.")
-class read_sequencer:
+
+class ReadSequencer:
     def __init__(self):
         self.sequences = {}
         self.reads = {}