From 200b8c6c03c00eebd5cb02c9088e6b0957878680 Mon Sep 17 00:00:00 2001
From: Christoph Harmel <christoph.harmel@unibas.ch>
Date: Fri, 11 Nov 2022 15:58:38 +0100
Subject: [PATCH] feat: added read_sequencer class, updated main() in cli.py
 accordingly

---
 read_sequencer_package/cli.py                 |  11 +-
 .../fasta_testfile/result.fasta               | 300 ++++++++++++++++++
 read_sequencer_package/generate_sequences.py  |  24 --
 read_sequencer_package/modules.py             |  47 ++-
 4 files changed, 347 insertions(+), 35 deletions(-)
 create mode 100644 read_sequencer_package/fasta_testfile/result.fasta
 delete mode 100644 read_sequencer_package/generate_sequences.py

diff --git a/read_sequencer_package/cli.py b/read_sequencer_package/cli.py
index f242c4c..e786d78 100644
--- a/read_sequencer_package/cli.py
+++ b/read_sequencer_package/cli.py
@@ -1,8 +1,8 @@
 import argparse
-from modules import run_read_sequencer
+from modules import read_sequencer as rs
 
 parser = argparse.ArgumentParser(prog='read_sequencer',
-                                 description='Simulates sequencing of a DNA sequences specified by an FASTA file.')
+                                 description='Simulates sequencing of DNA sequences specified by an FASTA file.')
 parser.add_argument('--input_file_path',
                     help='path to FASTA file')
 parser.add_argument('--output_file_path',
@@ -13,10 +13,11 @@ parser.add_argument('--read_length',
 
 args = parser.parse_args()
 
-
 def main():
-    run_read_sequencer(args.input_file_path, args.read_length, args.output_file_path)
-
+    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)
 
 if __name__ == '__main__':
     main()
diff --git a/read_sequencer_package/fasta_testfile/result.fasta b/read_sequencer_package/fasta_testfile/result.fasta
new file mode 100644
index 0000000..7b9bb49
--- /dev/null
+++ b/read_sequencer_package/fasta_testfile/result.fasta
@@ -0,0 +1,300 @@
+1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 481 bp
+tgagcactcggtgccaagggcggggatacacagatggttggctgatacaaccgggactta
+aattccctagactagatctgtgttggaacgcctctctacgagaaggcgaacgaactggcg
+ccgaggcgatcgctaacatcttcgtctcgcttgaaccacacaatggatgattcctcccta
+ggggtttgacaatcaacctggatagcgtttaatatagatggctggttgatttgtaaggcc
+ttcacagactactcagagcaataagtgaccccccaacaatcagaggctgatcctctgctc
+2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 495 bp
+ctgaatcaggtgtaggttctttttacgtcgtttaaggagctacacggtatcttgttttca
+gttaaggtgccacacccccgggtggatcatccgtcagctttcctacaattaggtaactgg
+cgggatcatttagtcttgtattaagacgctcgcgcccggggcggccggcttgtttgtgga
+gagaaacaacaagtctgagtatagattaaatacaactggtttactggcaagtcagcgcgt
+aacaaccggtgagccgctgcgcatgcttactgcaatgaacatcttggcacgatcctgcga
+3|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 193 bp
+acttcagtactggaaggatctaggaaccattaatgcgagtgtggtgacgccagacgaccc
+ccggtgttctgccaccttctttggataggagaaccgtcactcgccccggaggccccacgg
+ataagaagggtatcttgtgatcacgcgaatgactcacttgcgtaagtaatctaactttgt
+ttttcgctataaaAAGCCGGGGTGTTGAAGTCTATCGTCGATGGCTGCAGTATTAAAGAT
+CTTATGACTAATGCTCCAGCTTCCCCTCTGTGGTTAGAGACGAACTCGTCAGCCTCGATT
+4|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 625 bp
+acgtctggagcgtgggttgacccctgtacatggttctttccggatccttaacgtgccgat
+acaactcaaaggtaactgtgcttaccacttccgaagctacatgcctctaacaaagtactt
+tcgaggaggcactcaacccccggagatgctttgcgcggaagcagagatcgctgctcaaaa
+tttggaatcactttcgtgcgagacccaaacaatttatggtggattcaagcgaacgagtca
+tgattacagatctatcaatcgaggagaggacggcttcgccgtttccttttaatgtgaaac
+5|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 845 bp
+agagcgtacggcgcgcatcgtataccctacgagggcggcgtgtggaggaacgctgggctg
+acactgtagaagattagatacacttgtccctaaaattaacccttaaccgctattagccgt
+gaacgcttcctaatatttcaagccgtatagctaagtggagaatgtggagccctggtcaaa
+tcacgagccaattagccctagacggacagcacatctcgtcgcgttaagcggaacactcag
+cttttattacctagtgctcagcctggtttccatatgctctaaccgaactgatgcatactt
+6|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 703 bp
+tgcagtcgatgtgctattcgttttaggcagtctacgcgcttagtaactcccacggccata
+gacttatctcagacatggaccatgtcgatatcggacgccgtcttaccacatttttcatag
+cccttcataaggcagcgtgctcttactgcccaataaggtggacgattccgaccctaggcg
+aaccagcgctatagatggaccttctaattgatgcgcaacgtgattgtttccttggtctgg
+gttagcatttcggtagcctaacagtcactccagttcgctaactggcctggatgagggccc
+7|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 243 bp
+actctttagaatgggtttcactaatagtacgtgcatacaatttcgtcagaaagggcgctt
+gctaagggacacggatcaatgatgaccagacttatggtgtcaggtctcactatattacat
+atccggaacccgtgcccgcaccacgcgctgggtctaggcgaccggtgcatcatctccgcg
+tctctagaggattctctcggtaaatgctgaattgcgtgagatcaaatccgtatgccagtc
+atgAGGCAAGGCGTATAGATCTTTCCTCAGCATGAACCGGAACATCCTACAATCGCACGC
+8|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 863 bp
+attggcccggtccaggacagagccttatattgctactggtatgagaaccgttctgacgta
+aacttgatggctttacgcctgcacgggcttcatacacacatgaccgtggacaaagtcgcc
+caggccctcgaatagggtgtaatggttaacggttagtgccaccccaatgggtgcgaggca
+gtaagagtgtcctatggcaaaactctcctcgtttcagaagggtcgctcctctagcctcct
+tatcccccctataatagtactcgccgggtacgagccggagctccctcgagaagtcatcct
+9|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 494 bp
+aagcgaaactcctagaacttcccatcaggcaatcgtgtcccacgaagcacggatactacg
+ggcactagttgaatggggggtttttttcgtaggtcgtaataggtactcggatagtcggcc
+cagagttatgcttaagaatgcgctgcttaattcaatgtgactgccgttgtctccgatcag
+atccaggtgatgattgcgatcgcagcgacatatgtctcgaaagacgtgtcgtgaataagc
+ctgtaagcccaatgcaacatggttccctcaccttgtagctgatgtaccgtgtttcaatct
+10|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 86 bp
+atcctagcgccaaagatttactgttatggggtcgacgaacactagccgataatgccgtcc
+tgggatctctagcctagtattatgcgGACGTTTCCAGCCCCGCTGACCCTGAGTCGGACG
+TGAAAGCGAATCATCATATAAAGCATACACTGACTTGCACAAGTTGAAATAAGAGGTTCG
+CTTAGGCTTGCCTCTCTAGTGGCGCAGCAGTACTGAGTGGGTTCTACTTACTCTCTGGAC
+TCATGATCGTGTACACCGTGAAAGACGGCCCATGTGCCGTATATCTACCGTGCATAACCT
+11|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 360 bp
+cgcctgagggtcctaaatctgacgtatgatcgaagagattggaaggtcccggcgggtcac
+cccacgttgcgatcatggccaaggccatggtttgctcaaaaatcccacattcgccgtctt
+acgcgttaggacctcactatcccacagacggtgcgttaccttgtagttgacgcgggatcg
+tggtgataacagctatttccgagacttcatattcttttacatagcggcttaccgtagtga
+ctccatacattatttgcctattttgtagtgccccgaacagtaaggggaagccaactgccg
+12|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 140 bp
+gaattcctggggatttactcacccccgaggcggacaagatttccagctggatcaccgagg
+gttacttaatcccttcgatgctttcaaaggccctaatcagtattgagcaacgaaagcgga
+gtcgttagtgtccaagttgcAAATGGTATCGCAGAGCGGTCGGATTCGCCAAAAAGCTTG
+GCCAATGGCTAAAATTTAGCTCTCGCCCTCGCGGACATTGTGGACATGTGCCTGACTACC
+CATCATTCTCGCTCGGCACTAGGCCACCAGGGTTAACGATTTCGTAACAACGACCCGCAT
+13|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 832 bp
+aatactctcgttgaagcgtcggacagtaaagtgagagatttcggcccacggtagtcggac
+attctcagtggggagcgaagagttgcgcttagagccgacgtacacgatataacctcaatt
+gaaaatcgctatgtgcatcgttagggcctccggcgtgctgtttcggcagctgagtgtgag
+ggtataacttaccttcgacccgaattgtctcgcggaaatcctaggcaagtaatccacttt
+tggtacgggggagctagttcctctaagacgaacaagtgcactcttcacgtatagtgccct
+14|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 296 bp
+atcggggtgcgaaatcccctgagctggttgactacatacgtaaccacgttccgtgcgtca
+tctaagcgtatcggctcatactggtggtaactagacttggtgaaccctaggtgccggcat
+atcgaggtccgcatccaaaataactatcgctatagctacatagacatttactcgcaatat
+tacacgaaccgtacgtccctcggtattaacgtaatggttaaagtctctaattccgctgca
+gagcggcgggataaagacgccggtgtggcctgaatggtggatctgtccgtagtaccACGT
+15|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 515 bp
+accttcaatttgttcgcccgggacaagtagaaattactgtaaactaaacttaacctattc
+cttgttaaagtccgcaccaagtgtactgtaagaatggtcgctcgtaataataacgagaag
+atcctcgagccgtggtctgctgcaactaccttgagcggtacatcgatgtcccactctggg
+cggggatcaggggcgagacttgtggtgaggccaaagaatggcgcatatgtaggcaccata
+cgtcgatacgttccaggagtagaggcctcgaacatacaccacgataagtctacagacgca
+16|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 820 bp
+ccggctcaatcctgtagaaccgcgtacaacacacccaagctataccgcacacggcgcctt
+agcaaccactgcttatctgcgtattatacctttacaatcattacatttgatctatctgtg
+taccggttttttttgattcaattcgctggattacgacctcccggccaaaaattctcaatt
+catcgttaacagacgtatttgaagataatcattcaacgtgaactagcacttggtcacttg
+gtacgccaaccaagctgtgctttggggcaaccctttataactcacatgccgtcctaggac
+17|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 791 bp
+attgttagggcctgtccggaaaagatcaacggaagatattcaccagcacctatgctgact
+cacgtagttcccgacgttcagtcccctccaacgtggaaggtaggacccatctccttaacg
+ggatcgatcggtcttcctgtgaaagttgctcagagtcctcaaggacgtttttgggtgcgt
+gtacggtatggttatggtacgtgtctgtgacagagggtattcttactggttaagtgaccc
+atatgaccacctgacgcccgagcatagacctgtaggggtcgacgcgagagatggcagctt
+18|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 328 bp
+accgattacaggcagtcggccttgtccgctcgtatatccagggatgttccaccgaaagtg
+ggagtgtggcacttattggtaaaaggcatttttacgaacgacactgataggattgatcac
+tcaagaaatgttctcgaccctgaggtaggagtcttaacagacggacatcctccgtagata
+cgtgagaattaagggacgcatgtcgaaaacgcttggaatctactgtagtggcccacctta
+cgcttcttccaataactcccttcatagtccggcaacctcggtgggggtttcccttaggcc
+19|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
+ggagtggaaaattctgtagtccgttggcggcgaccgcaaaccagaataatatggtcacgt
+taggccctcgggccccttcatatgtacggagtcattgaattagcattatactaccgttac
+gcaagaccctatcccatccgcgactgtcaccactgctgtaaggttgcaaggctgtttcaa
+tgtaaagtaggcgaattctgacgtgggctgataacgaatcccccgggttatctagtgcaa
+gtgctatccCAGCAGTAGCTGTTGACTCGGAGGCGTCAGAACTTCCCTCTAGTGTGGCAA
+20|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 440 bp
+atcttaaacagcccaatcggctcgccgaccaatttcccgcttcacagtacgcggaagaat
+ctgcagatagaagtcagccctctcacgtcaataggaatgctgcccgtcatgtttaactac
+tcaagttttaaggtgtcccttatcggttccaggatcatgtctgaaggaagatggtcgcaa
+cgaaatctggagtggcatacatcgttcggtcgaagcataatctcagacgttatctataaa
+gttagggcgctgtatggattgggattcaagctcgaagcctgttcctgccatacagcgcct
+21|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 840 bp
+cataactcgtgagtggccctgtacaagtcattgcatcacaatccttgcaatttgctcctt
+tggccaagcgtacaagaccccggacccatacgctcccggctgataaactgctacagcatg
+gtatatccggatgatgcccctgaaaactgcggaagtcaatttgttgatgaatccccgact
+ttccgctgttcctgtggatggtcgaatgccaaatgaagagctgctccccccttctttaat
+atcaagcactacaaagataaagcctgtttggctgacggcgagccctcccctatcgtacgc
+22|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 234 bp
+caccgcgaaagtgactcagttttcccggtcttatcacggtcgttgtcgtccagattccgg
+ttgttaactgcgggagctataacacttattccttactgcgacggctgatccactaagaac
+agttcatagagctcggctatataatttgaagacatagattccacggtacttgtagcccat
+aaccgctgaggaggaacgtccaacggttcgcgcggagcatgtgacgcttaaaggGATGTA
+AACAAAAGTTTCCAGGCGGCGGCGGTGTAGGCCGTTGCACTGTACTAGGCACAGCTACTG
+23|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 917 bp
+atcaagtgattacctggtaacccgccgctcttgcagtgttcaccctttgtgtcgtcttag
+tgtttgtacacgttaaggaaaagcgttagcttaaccattacgccccccaaagcccggtgt
+gtagttatctacatgccgtgtcaaagcggtgactaaatgtttatcaagttctgatgacaa
+cgtgagctcttaaagccattgactagtataagcacggaacaatgataccaggcaagcttg
+aatataggataaggcctctaagctcgaagcggatcttacggaggtgtgaatcaacagcac
+24|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 676 bp
+cacacggcatcgcaaagcgagctatccagagatgatacatgtggttgaaggtgattgcgt
+caacatgggggttgctcagtttggttggtcaatcaacggtggcagaccatgcgataacga
+tgatggtaagactgtaaggtaagttaaatactctcgtctgccagttgggtcgtcaacgct
+gcagagacgccattcttcccagaaggtccgagctttctacagtgccgcggcgtcatgacc
+aaaggggtccaacctcgcagtaaaatgtctatgcttctggtttggaatgagaccgggcca
+25|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 870 bp
+ctgatcaccaatagcttgcgcttaacacacgcgccttacaattatatgacgcccttgcca
+atgacagatagagccattaatcgtggaaaccaggcatttatacttgtccgatgtatcgat
+tctcctctatctacagagcccggacatgcgaaatatcaaaattccatgtatactgaataa
+atacattgggcaagccgggctcatgcagcaatcccagcgttgccttacgcaaagatatct
+tacggagttgcctttagattaacagcacgtgttcaaaaacctagccaactctgtcggtct
+26|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 751 bp
+gggtgcgttatggggactaaagactgttactaccggtactccgccttatagagccgtcac
+gtattaatcagctatcaacagatactatcgtcacagccctccttctggcgaaggatctga
+gcatttgcaaagctataagttggtacgcaacggtagagggcttcgtagtcggggaaaggg
+cttgcagtagtataggccgtaacttatctgttgcaacctcaaccgcacgaatcgattact
+ctataactgccctcaatacagtatggttaccagtcaccttcacactgaagattaattcgc
+27|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 574 bp
+gtactgcaccttgcactgctatctacaatgccgagggtcgccctagtgctttgcatgttt
+ggcctctacctacgagtctacgcgggcgtttttaagcaagctacgatcatcttgatccaa
+gggtacgaggccccgcagaccaatggaggtcgtgaccaccctcgtgtatgcctcgcacta
+agcgagcattctggtatactgtctctctcctgtgataataacagtcggctcgatattcag
+ttcacatgaaacagtatgttatataggtgggatggttataacacggaaaggtgaaaaaga
+28|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 169 bp
+agctccctaaacaacacccgcgtaaaaccttcagttatggtgccgactaaccctgtggat
+gtcttagcgctctcgttccgatgggtgctgatactagtaaatgagactcgagaccgagaa
+cacgcaacggctacaacctggtcggttgttggggtttttataatcagtgTACGAAATAGT
+AGACCTCGCCCTGTAGTTGGAAATTACCGTCATTGGTCTATACAAAGCGCGTGCTTCAGG
+ACTCGGTGCCGAATCACTCCGTGCCAAATTAACGAAAGCTTCTGATGTGGATATGAGTTC
+29|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 408 bp
+tgcagtgatgcatcgataagaccgcatagttacctccttacaggtgacgctaggctaatt
+gggagtgctggcacttgtgccctacagtcaagcgctcacgcggtgttctcctcccgcaat
+cttagatattaggctctgtaccgcacgaaggatgaattttcttgactattggtccctgtt
+tacgagggcttacctagagtgaggatgaacataaacaaggcctacttgacttaaggcttc
+caaatcacttgagggcaaatgactcctcaaacgcgagtgccagtactatccgtgagggaa
+30|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 52 bp
+caaagcgattcgggttaacgcacttaagagttcgacgtaggttagtcccctcTGAAGCTG
+GCCATAACAGGCAAGTTATTGATTGGACCTTACGACGTACATGGCATTGCGAGACACGGA
+AGCTTGAGCACTCATAGATCTGCCAGTCCCAACGCAAGTTGTTTTTCCCGCATCATTCAG
+AAGAAGAAGACGGATTGAACCAAACTGTCATATCAGTGGTTAGCTGCTGTAAATTCAGCG
+GATTGAGGGATGGGTTTTTCGGAACATTATCTTAGCGGGAACAATAAATGCGAAAACCAG
+31|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 581 bp
+tgctctgacgtgtaagcgccttcgataacgtctttgcagcgccccacaaagtaaggaccg
+gtctaacagggcttccgaatcaatagactgatagtaatgggatcctgaggctgggacccg
+acacacggcatattttactagaaacgctgatttaaactccaattatccttgacgcactga
+gccacagtcttagacgcagaatgtccgcaggagccctgtctttcccctaaatcattcgcg
+gcatttgtttacgggttaagtcctgcggatcctagagtctgggccccgtacaaccaggaa
+32|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
+gcggaactacctctctaagaccgcacaacaagtgtagtagatgaagatcacgcagagtgc
+tcggcactgcatttttatacgtcgaatcagaaacgaggttcctcctctaggcttgttaaa
+aatccgggcgcgatgggctggtaatctgtggccatgggagcctcgccatttaaagatttt
+ggttaaggctcctctgttgtgtccatcacccttgaacgagcccgtacaaaccgtgtacga
+tgttgacacTGCAGAGAGGGCGTTTCGTACCATAACATGCATCCTAGGCGGTCATATTGT
+33|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 297 bp
+gccctcgcgccagcttacttttagaaaacatcgaccggtaagagatacctgggtgagctg
+ggcttcacgacatgttcttaaatcaatactctaaatctgctttgtagcatgcctcaagta
+aaaaaatgtgctggttccgcacaggtgtgacgattaacgttgcgcccgtttgcgtcagtc
+cagatcaccgatcttccacaccaccggtgggctgccggactgcaggtaatgactcctggc
+tgcattctctgacataaaggttgaatagaacggcgtccttgagaaggttatggaacgAAA
+34|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 573 bp
+gcctaggggtcttgaccacagggagtacgagcattgatcattggagcaggtggctaatat
+tgatagtggttagaccaccggcgcatcatcgtacgagcgcgggcgatacgtgtctttcac
+cggcgcactaatcttatcttacttctcaagccccgacagcatgtacgccaagtgttgttc
+tgatgaaactttcgaaatagcaactgttagtcagttatagttggggagggcagtgaatac
+ctcaaatacacccaagaaataacttcgaagcggcgcctatatcacacccctgtttcttat
+35|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 559 bp
+gaaaaagtcgccccattcagttacaatcgtcttcagaagccagctcggttggggctatct
+gcggggtaatgcaacagggggctaccagacggtaaaccagggtcttgctattggtgttac
+gaaacaaaggagctatgcgacctcattagatcgagattactctcacaggcagctccggcc
+atagcacaactaatttcgggtgtggagctcaccacaggaacatcttgtgcgtcctttgtt
+atttaattgtgcattgtaatgcaccggaccccgggaacatacagccattatctgtgttgc
+36|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 187 bp
+ctaagtccttatctatgatgcatctttcgttactgcgacaatatccgagacgagcagagt
+tacacgccgaggtgtaaacgaatacgattgctatatgcaacgagttggttacacgcgtga
+aggcgaatgtggatgctgcacttggagtcccattttaccggccgcacgtgctagctcact
+caccttgCAGATATACACAGCTCGGGGCTTATGTGAGGGCTTTCTGTAGATCGGGAGCTT
+ACCAAAATATTATGGCAAGGACTCACACTTTGATATACGCTTCACAATACTAAGTCCAGT
+37|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 549 bp
+ttcatatggggatttggaatcgggtttgtgcggaatatgcccacgagactgcttatgtca
+acgagacgacccattgtcacgttgtaaggccaccaataacacacaggtcttcgtttgctg
+tctcagggcaatcgcatcgacaacatcgtatggataccgttttttatcagcttacggcgc
+atcatactaataaggtgtttgagagggcgcagactcgaagcagtgtgatcttcccggttc
+gaagatgcaaaaacggtcctatttcgatccaaaactcagcgcactagtccaatgcttttt
+38|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 916 bp
+gtggcctaccataaatcaatttgggttaacgctctttgatctacgcactatgttgattca
+cttaccccttgtcaccgggcagaagagagccagtttaggtgtggttgtatttgccaaacc
+gcaaaccgcctaatgagctggatccggccatggaattaatcccgtcgtttgactcgaggt
+gttcaaagactgtgcaacacgacgtgcattcatcactagaacttaatctagaccaggcct
+tgtggccaggagaggcgacgtgatattgccctatacacagataattatatacccctcgcg
+39|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 848 bp
+accccggtcgctttggccggtcgtagccctaatcaattctgttcgtatcactaaagtaac
+ggtttgaaatcctttgcaaacttgatctgggtatatgaaccggtatgcggggatagtggt
+aaataagtagtttacgagctgagcgtggattatcccagagaagttgccttaggtccagag
+cccgcacctacaatcactcgaggccggtcgagcgttgcgtggcaaggaaacccagccggt
+caccctaccctcaaactcacgtcattgatccaatcatacatggcgtctctcacggtggtg
+40|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 289 bp
+agagcaaaagaaagtctgctccgcgtgacacacttgctcgttgtagtaactgcacgcgcc
+gtctactcgacagggaccccccgtcggttcctctctatagcaatcgcggaagtggttccc
+tgcctcccgcgcagaagttcaaactagtaatccttaatgacttgtggggggggagatcag
+tttcttccacaatggagtaaacttatgcgagaatcaagatcgcagaggccattttttgat
+gatactgtcagatatgtggttagccgtatcacgttaccgacgcagaattTGGTGAAATAG
+41|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 642 bp
+ctggggaatgaccgtaccgatctaattccccgtcgaaaaacttatgacgcgcagttgtcc
+ttatgcttgagacatgaatccttgccccatattggcgatcttggccaatgagatctgtcg
+aaagtactggaggccggtaaattgggggctctagaggtccgcccctgaaggactaacgtg
+tgtgtgtgtctacgtgtcgggttatcagcgtgttggacgatggccgtggattcaacgcat
+gctagagagctaatgatcctccgaagtcaaaagcctcagtgcttcgatttatgagcgcgt
+42|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 993 bp
+gcaagaagccaaaaaccttgcaggaggtcatttaagtttacccgcgcataagcagagacg
+gacctctctgagatctcgcaccgcgcgcccggccggcactatcgatgctagactagggtt
+ggtgactagcccgtcaaaaccagcctaaacgcaaagattgtaggcgctagtccggaactg
+actgcttcgtgtcggtgggagcctagtatgtttccgggtctatgacccctaaaatcatag
+acgtgtcttaatagctatacctgacttactttgaagtacttgccacgacgagtttatgag
+43|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 473 bp
+ggttgtccaggcgcgagcaagtagctgactcgctaatcttaacgagtattgcttaggact
+tccaaatactccaagacgtcaatacgctttatctttgtgaagtcatcccggaccgagcgc
+ttgggtcgtgatttaaaatcccctgtgatgtggctacaggtgcggcctatacagccgaga
+agaaggccgtctttaggcgtccaatgaaccgttacagggacacaccaaactgcgccaact
+gatcccacgggtcacggtacgctctaagaccagtcgggattctgacttaacatcgcagca
+44|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 272 bp
+gtagaacttgttccccatggacaatgctagttccgttaatgccaggtattcatgtgccaa
+gcgcctgcctggggaatacgagcctctctacaaacttacggccaccatgcttaaagattc
+ggtgacttcactaatgacctatacaagtaatgcggaggacgctgtcgcttattgctcttt
+gctaaggccagttatgtccgtcagtcaacgatacgctgcggcggtgggtgacggcactag
+accggaagcctgatgacaagttcgaatcaataGTCGCTTCCATTACACTTGCGCTATTCC
+45|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 860 bp
+aaaagcatcactctaacgacgctaccgtctgaatagatcaagattgctatcggttcgacc
+ttgatcgcatgtgaacccgcccaaaaacccgtctcgacaaaagttacgtcgcatgggctg
+cgccaccggatagctcctagcttatcttataaatcaggtagagctacaacatggtgctat
+gacaactggagtgtcatcgctttggcgaaaccgtaaagggtgggaattgctgcattctca
+actgggccgaactattccgcattcggctgctcacaaatcgtggaatgtgtccttgaacgt
+46|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 884 bp
+aagcctctacaggctctgcggtttggctttacttaacggtgagtcaggaaaacattactg
+ctacgttcaccgtgttcagagatagagagtacattagggaccaatcacaacgttcgccag
+ggcaccgcctaatccgcgttgttagcaagagtacaggctctcgtatactttcagaccctt
+caatactagacgacaaattgcagcccggggtcatcggtcgactcagatacgtgctaacga
+gtaccaggtctaccgttgcaacgttggatgcgttatactcggcataaggcgatgcccttt
+47|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 888 bp
+gcgccttgaagaggcgaggtctaaaggcaaaaatttagatccgccctatgagacggccga
+cgcggagaattccctaaccactattgtcctctgcatcgatatcaggaataggcttacctg
+caatctcttatggtgatagactgtttgggagctgaacctgagacgcgcacgaaatttgga
+aggatcaaataggccccgcagtctctggtagacttctgccgagcggactagcttggctaa
+ggtgtacaagcctaaatcgtttttcacatcaattttatagctgattatagaggaacgacg
+48|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 588 bp
+catcaagatgggttacgtaggaccgagattcagtctctgggttagagccgacagcggggc
+cgctacatagtacacggcgaggaatgcggggttgggctgaaccgtacacagtgggctagc
+tgcggtacctgccaccggcatgcgtttaaatcctttcctttggcgaagccaactgccgac
+gtccgcaacagagactcgttttccgaccccgttactaaatcagctaactggcgcctgaat
+cctcttacgtcggatgttaattagtgtatagaatatcggagggttgagtgcgacgcgctt
+49|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 626 bp
+taacctcagtctcgttcccccctcggtagttcggacccttattcgcttatctcacattca
+tcactgtagaccaaggaccgggcatacttgcggatatctaccaggactaggcacttaggg
+atacgctgttgaatacgggtttcgtcccgtgtactcaagtgtagtttaagataggtacga
+gtgctagtacatcgtacaatttacaactgacttaaacgagagtttattatgtcttgttca
+cttgttgacacgcctgggaaaataataaaaggcaacgtctaatctcagacccgttgatta
+50|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 214 bp
+taactgtcggtcactgctcatcccgactagttcggctcactagacttactcgcggaagcg
+agaagtaggacgtcgtgtaatactccaacgtcgttacgcaatgttgtaaaacttcatcgc
+attccgtgcatggcctaaacgtgcagcattatataacgctctttggtcttaatatccatc
+gcgggagtaacgcgaaggggagacgtgtgcctgaACGAACGCTAAACTAGGTACTAAGTC
+GTGAAGCTCGGGTGGAGACAGGTAAACTGATCGCAACGTATCAACCAATTCTGGACCCTA
diff --git a/read_sequencer_package/generate_sequences.py b/read_sequencer_package/generate_sequences.py
deleted file mode 100644
index 0125bbf..0000000
--- a/read_sequencer_package/generate_sequences.py
+++ /dev/null
@@ -1,24 +0,0 @@
-import random
-
-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): standart deviation of length of sequence (gaussian distribution).
-
-    Returns:
-        list: of n sequences
-    """
-    dict1 = {}
-    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
-
diff --git a/read_sequencer_package/modules.py b/read_sequencer_package/modules.py
index ca84a64..854aaee 100644
--- a/read_sequencer_package/modules.py
+++ b/read_sequencer_package/modules.py
@@ -1,3 +1,26 @@
+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
+    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):
     '''
@@ -36,7 +59,7 @@ def read_sequence(seq, read_length, padding_probabilities=None):
     if read_length >= len(seq):
         for nt in range(len(seq)):
             sequenced += seq[nt]
-        for nt in range(len(seq),read_length):
+        for nt in range(len(seq), read_length):
             sequenced += choice(bases)
     else:
         for nt in range(read_length):
@@ -47,7 +70,7 @@ def read_sequence(seq, read_length, padding_probabilities=None):
 def simulate_sequencing(sequences, read_length):
     results = {}
     for index, key in enumerate(sequences):
-        results[key] = read_sequence(sequences[key],read_length=read_length)
+        results[key] = read_sequence(sequences[key], read_length=read_length)
 
     return results
 
@@ -63,7 +86,19 @@ def write_fasta(sequences, file_path):
             outfile.write("\n".join(wrap(value, 60)))
             outfile.write("\n")
 
-def run_read_sequencer(input_file_path, read_length, output_file_path):
-    sequences = read_in_fasta(input_file_path)
-    reads = simulate_sequencing(sequences, read_length)
-    write_fasta(reads, output_file_path)
+class read_sequencer:
+    def __init__(self):
+        self.sequences = {}
+        self.reads = {}
+
+    def add_random_sequences(self, n, mean, sd):
+        self.sequences = generate_sequences(n, mean, sd)
+
+    def read_fasta(self, input_file):
+        self.sequences = read_in_fasta(input_file)
+
+    def run_sequencing(self, read_length):
+        self.reads = simulate_sequencing(self.sequences, read_length)
+
+    def write_fasta(self, output_file_path):
+        write_fasta(self.reads, output_file_path)
-- 
GitLab