diff --git a/.gitignore b/.gitignore
index af56f610571e02b53c6a162316a0555ecf63a845..e67a40ec0cbb5aa7e77e9607e08a517dc1187296 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
.DS_Store
.idea/
+__pycache__/
diff --git a/read_sequencer_package/cli.py b/read_sequencer_package/cli.py
index 8273b5565d3efdcc95061d7ffa237f39c41aad0e..f242c4c1f4058c5f6baf5f3e7f675f784308c26a 100644
--- a/read_sequencer_package/cli.py
+++ b/read_sequencer_package/cli.py
@@ -1,11 +1,22 @@
import argparse
+from modules import run_read_sequencer
-parser = argparse.ArgumentParser(prog= 'read_sequencer', description='Simulates Sequenceing of a FASTA file.')
-parser.add_argument('--file_path',
- help='path to FASTA file', action='store_const')
+parser = argparse.ArgumentParser(prog='read_sequencer',
+ description='Simulates sequencing of a DNA sequences specified by an FASTA file.')
+parser.add_argument('--input_file_path',
+ help='path to FASTA file')
+parser.add_argument('--output_file_path',
+ help='path to FASTA file')
parser.add_argument('--read_length',
- help='read length for sequencing', action='store_const')
-
+ help='read length for sequencing',
+ type=int)
args = parser.parse_args()
-print(args.file_path, args.read_length)
+
+
+def main():
+ run_read_sequencer(args.input_file_path, args.read_length, args.output_file_path)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/read_sequencer_package/fasta_testfile/50_seqs_50_1000_bp.fasta b/read_sequencer_package/fasta_testfile/50_seqs_50_1000_bp.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..12e41cdac4403ac3c51f4f76553889346ab56bdf
--- /dev/null
+++ b/read_sequencer_package/fasta_testfile/50_seqs_50_1000_bp.fasta
@@ -0,0 +1 @@
+>1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 481 bp
tgagcactcggtgccaagggcggggatacacagatggttggctgatacaaccgggacttaaattccctagactagatctgtgttggaacgcctctctacgagaaggcgaacgaactggcgccgaggcgatcgctaacatcttcgtctcgcttgaaccacacaatggatgattcctccctaggggtttgacaatcaacctggatagcgtttaatatagatggctggttgatttgtaaggccttcacagactactcagagcaataagtgaccccccaacaatcagaggctgatcctctgctccgaaggcagcactcatcatcggtattctgttcgctagaacagatggaatgcatgcgccccgctaagtttgattgagttaaacttattgtcttatagccatagccaaggtatctatggtgtcgtacgtgacagttccgtgtaggcatgccatcccgcctcatgcgtcatgtcatactgaggc
>2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 495 bp
ctgaatcaggtgtaggttctttttacgtcgtttaaggagctacacggtatcttgttttcagttaaggtgccacacccccgggtggatcatccgtcagctttcctacaattaggtaactggcgggatcatttagtcttgtattaagacgctcgcgcccggggcggccggcttgtttgtggagagaaacaacaagtctgagtatagattaaatacaactggtttactggcaagtcagcgcgtaacaaccggtgagccgctgcgcatgcttactgcaatgaacatcttggcacgatcctgcgatagcgtgccctgacccgtgcacctcgtcggtgaatttcgtcgaacaagcggatcgccacgccacgtgagatcaagccaaaacacaaaaaccacaggcaatagcgacgctgaagtgtcatttcctacctaaaacttcggttcttcttcttaagagggcattaagtccggataactactgcatggcacctgtgtatg
>3|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 193 bp
acttcagtactggaaggatctaggaaccattaatgcgagtgtggtgacgccagacgacccccggtgttctgccaccttctttggataggagaaccgtcactcgccccggaggccccacggataagaagggtatcttgtgatcacgcgaatgactcacttgcgtaagtaatctaactttgtttttcgctataaa
>4|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 625 bp
acgtctggagcgtgggttgacccctgtacatggttctttccggatccttaacgtgccgatacaactcaaaggtaactgtgcttaccacttccgaagctacatgcctctaacaaagtactttcgaggaggcactcaacccccggagatgctttgcgcggaagcagagatcgctgctcaaaatttggaatcactttcgtgcgagacccaaacaatttatggtggattcaagcgaacgagtcatgattacagatctatcaatcgaggagaggacggcttcgccgtttccttttaatgtgaaactagagccttcctcaatagtgaggcccttgcccggtgcccgggattggctcaaaagtaccggctcaggaagtctctcaactgccaagttggttaaagtagcttcggcgtaaggaacccgaccgaccatcagtgtcatacaaggaaatatttccaggaacctagtttatcttgaagttctgaatgagttaggtaatgtcggcccttcatgacagggggacgtgctcgcgagctcaaaccaagggggctaagggcgacggtgcttagtcatctactagatccacccacatgacgattgtgtgggtcctttcagccttttacttctcgc
>5|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 845 bp
agagcgtacggcgcgcatcgtataccctacgagggcggcgtgtggaggaacgctgggctgacactgtagaagattagatacacttgtccctaaaattaacccttaaccgctattagccgtgaacgcttcctaatatttcaagccgtatagctaagtggagaatgtggagccctggtcaaatcacgagccaattagccctagacggacagcacatctcgtcgcgttaagcggaacactcagcttttattacctagtgctcagcctggtttccatatgctctaaccgaactgatgcatacttgggtctgactaagggccatggttcgcgtcaagcaggccgggttcagaagccctggttgaggggcggatactccagtcgcccgcaggtcgcgatccctgggtttaaactacttcacgacacgtacaaacacttactacctacccctacaacactgagtgaaaagtgctagctaagtatgtccgtcgagataggactcgactttagaggtctgcacgaatgtcctggtaggatgcccaccaaagggaataatccttcgggtacgttttgggcaggtgtgacgtgagaaatccgcacccttatcgccgtaaaggttatttgcggggtgcgtggttacttgagttgtccctctcgagcggggtaacaaaaacctactgtatatctagtctggtccgaaattctttatgctgccgacatgctgcgacccgactacgtgtgtaagagtcattatttcttaatagtttaacaaggctacacccctatatgataaaggctattctccatagtgtaagagtctgttgcaccgacaacccggcgtctggctacat
>6|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 703 bp
tgcagtcgatgtgctattcgttttaggcagtctacgcgcttagtaactcccacggccatagacttatctcagacatggaccatgtcgatatcggacgccgtcttaccacatttttcatagcccttcataaggcagcgtgctcttactgcccaataaggtggacgattccgaccctaggcgaaccagcgctatagatggaccttctaattgatgcgcaacgtgattgtttccttggtctgggttagcatttcggtagcctaacagtcactccagttcgctaactggcctggatgagggccccatactatatggtgatagcaacgacaccccagtgtattgacctgttgtgtcctggtgatgttgaacgtcaccaagatagtctctatgtgactccatagctaaggagggtgacgtgatgcgccggccccgccccagacactgctacagaaagcttaaggcgagcgtatgaagagcctttgggcatacactctcgtatctagctaggtcaaggtgacggaatgaatctgctatatctagattggcacgcgataatctaggccaattgctggtaaaacacatggtcttattgtatacccaatcccgatttgaatttcctgcaacgaggcagctcgcagaggaacttaagtagagtgaaccctggagccgaatcccagagtcgtcggggacaaagtatatgcaacgg
>7|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 243 bp
actctttagaatgggtttcactaatagtacgtgcatacaatttcgtcagaaagggcgcttgctaagggacacggatcaatgatgaccagacttatggtgtcaggtctcactatattacatatccggaacccgtgcccgcaccacgcgctgggtctaggcgaccggtgcatcatctccgcgtctctagaggattctctcggtaaatgctgaattgcgtgagatcaaatccgtatgccagtcatg
>8|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 863 bp
attggcccggtccaggacagagccttatattgctactggtatgagaaccgttctgacgtaaacttgatggctttacgcctgcacgggcttcatacacacatgaccgtggacaaagtcgcccaggccctcgaatagggtgtaatggttaacggttagtgccaccccaatgggtgcgaggcagtaagagtgtcctatggcaaaactctcctcgtttcagaagggtcgctcctctagcctccttatcccccctataatagtactcgccgggtacgagccggagctccctcgagaagtcatcctgctcttaccacaggcagagaacgcgcaaggtttagatactaacttcattcatccaccagctggacaaggaactatagagagatgacattaggttatagctgaggggcgatcccattacccgaggctcgcaatagccttctactctgccaatgatcagtattgtaaacatggctggcgtccctaaatacaaagtcccgctgcaattgatggacttagacgaatcactagcaaagtcgataaatgtttacgctatccaatcccgcggttttaaaggtctgtactatacattcaatacggggggagatgtgtattgagccactagaggtatctaatgggggattgaaaaccgttttatagtcagtctaagcagcgccccttatgtcgctgtgatcggcagggttttttccgagatgtaaggcgaccgatatttcgttcttggcttggaagtagtacccgcgatgacctaccaagtagtccgacccattgatagactatggataccgctcccctccggtcacgaagcaccttagtgaggcatccgccgtgatgtgttgtttggagtg
>9|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 494 bp
aagcgaaactcctagaacttcccatcaggcaatcgtgtcccacgaagcacggatactacgggcactagttgaatggggggtttttttcgtaggtcgtaataggtactcggatagtcggcccagagttatgcttaagaatgcgctgcttaattcaatgtgactgccgttgtctccgatcagatccaggtgatgattgcgatcgcagcgacatatgtctcgaaagacgtgtcgtgaataagcctgtaagcccaatgcaacatggttccctcaccttgtagctgatgtaccgtgtttcaatctccgcggctatcgatcgccctttcatgcaagctgtaaccagacaggaatctgccctgccatcgttatgtatgcgtattacgactgattcgcgcaggcatcccggctaaggccactgggtataatccacagacattgcacgtcatatagaaaacgacctgtgttcacaatcagcccggggggagtcagagtagtat
>10|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 86 bp
atcctagcgccaaagatttactgttatggggtcgacgaacactagccgataatgccgtcctgggatctctagcctagtattatgcg
>11|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 360 bp
cgcctgagggtcctaaatctgacgtatgatcgaagagattggaaggtcccggcgggtcaccccacgttgcgatcatggccaaggccatggtttgctcaaaaatcccacattcgccgtcttacgcgttaggacctcactatcccacagacggtgcgttaccttgtagttgacgcgggatcgtggtgataacagctatttccgagacttcatattcttttacatagcggcttaccgtagtgactccatacattatttgcctattttgtagtgccccgaacagtaaggggaagccaactgccgcggtagctcatagacagacgtggtatacacgctacaaataagcagtggattgagacatga
>12|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 140 bp
gaattcctggggatttactcacccccgaggcggacaagatttccagctggatcaccgagggttacttaatcccttcgatgctttcaaaggccctaatcagtattgagcaacgaaagcggagtcgttagtgtccaagttgc
>13|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 832 bp
aatactctcgttgaagcgtcggacagtaaagtgagagatttcggcccacggtagtcggacattctcagtggggagcgaagagttgcgcttagagccgacgtacacgatataacctcaattgaaaatcgctatgtgcatcgttagggcctccggcgtgctgtttcggcagctgagtgtgagggtataacttaccttcgacccgaattgtctcgcggaaatcctaggcaagtaatccacttttggtacgggggagctagttcctctaagacgaacaagtgcactcttcacgtatagtgccctacagttgcgctgttcatggaatccgactaatagaccagtcccgaccccagtgcttcgactgttacaacagttatcgtcgcgcttcgggacgaaatctcggcattactatactcgacatacacagaaagctatggaggtcgccgtaatattcacctcgtcgagtctgtaggcgtagtaaacgttacataatagctaatgggactttcgaacggaacattatactcatcgtgaaacgtttggtcaccacactgtagaatccacctggatcggtgctagttctagtcattatgccctctaatactggtcgcgtagcagggcgcaaggtacagtgcgataccggaataggggtccacacctcacgtccacgtacctatagtcacgccgtatcgaattcattgcactccttttaagtattgagcgacgactggcacccggaatagttagtttgttcggaacgcccccacgcacgagtcgtgcgaattgaatgccgttagaacttggtgcatgcgccgtcgctactattaacggacag
>14|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 296 bp
atcggggtgcgaaatcccctgagctggttgactacatacgtaaccacgttccgtgcgtcatctaagcgtatcggctcatactggtggtaactagacttggtgaaccctaggtgccggcatatcgaggtccgcatccaaaataactatcgctatagctacatagacatttactcgcaatattacacgaaccgtacgtccctcggtattaacgtaatggttaaagtctctaattccgctgcagagcggcgggataaagacgccggtgtggcctgaatggtggatctgtccgtagtacc
>15|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 515 bp
accttcaatttgttcgcccgggacaagtagaaattactgtaaactaaacttaacctattccttgttaaagtccgcaccaagtgtactgtaagaatggtcgctcgtaataataacgagaagatcctcgagccgtggtctgctgcaactaccttgagcggtacatcgatgtcccactctgggcggggatcaggggcgagacttgtggtgaggccaaagaatggcgcatatgtaggcaccatacgtcgatacgttccaggagtagaggcctcgaacatacaccacgataagtctacagacgcatagatgacgtggaactcgcatctaacccctggaattctctgactgtcaccctgagccttggtgggccaccgttagggacgtgcaactaccctttctggtgcgaatctcgtttccttagtgccttcacacaaggaggccaattgtttgctaccccatccagacatttgggcattcttgtgagtcccgtaagtcggtcatgatgggtttaagttagt
>16|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 820 bp
ccggctcaatcctgtagaaccgcgtacaacacacccaagctataccgcacacggcgccttagcaaccactgcttatctgcgtattatacctttacaatcattacatttgatctatctgtgtaccggttttttttgattcaattcgctggattacgacctcccggccaaaaattctcaattcatcgttaacagacgtatttgaagataatcattcaacgtgaactagcacttggtcacttggtacgccaaccaagctgtgctttggggcaaccctttataactcacatgccgtcctaggactttacctagtccacctagcgtgttacagataccgattgcatcaagtcctcgacggaccgcactcgtcgcagttaaaggcaggtctatcagggagataccgtgtgttgcgccaattaatcttagaaaattatgcttgcaatagagcaggaaccctgaaagaatatggttctgtgaaaaagcgtgcactcccgtgtgtgctcgttggttactagcaccgacgttgggtgggcggaggggtcatatgcctgcgccgatcgatatagcgacgctcgtatcaagttgtactgcggcaacacgggtggctcggtgtagaaataaaacgggtgccctcgggtcgaagcgaagcgcaaatgctcgtgggccggagcggccgggggcgggccactatgggcattacaagccagacaggtaagagggagtgctttgatgtgaacagcaccccttccgctggacggggttatgacaagttcgccaagattttacaatatccttaacagtggaatgtccttaccgggtttac
>17|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 791 bp
attgttagggcctgtccggaaaagatcaacggaagatattcaccagcacctatgctgactcacgtagttcccgacgttcagtcccctccaacgtggaaggtaggacccatctccttaacgggatcgatcggtcttcctgtgaaagttgctcagagtcctcaaggacgtttttgggtgcgtgtacggtatggttatggtacgtgtctgtgacagagggtattcttactggttaagtgacccatatgaccacctgacgcccgagcatagacctgtaggggtcgacgcgagagatggcagcttttgtcatatcatcggttcatgtcaaggttggaggaattcaggcatacacaatctcggcttagtctgcgctgctcctgtccatacctggcacttggagtcaatggattcccaaaaccgacaaatgagtcaacgctctactttttgtttgctggaacgaggcaatatccattgattcccttctcaacaaatgttatcgcggcaggaggacacaccggggccgcccgggcatcgattcgtaaccgcctgaatgtgatacaaccgataatccacttgtaagaaaatgtattctagggacttggcaccgtacggtatagtagctaatctatctaccgctagctcccggcgaaacatctggcggctaacgaccgcacacgtccaagtaattatcggcactgcgatctgagggatcatctcgcggacggagattaactagttaagaatacctatctccatcgcaatgcgactgtagccaatagctatttaaggcgtgt
>18|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 328 bp
accgattacaggcagtcggccttgtccgctcgtatatccagggatgttccaccgaaagtgggagtgtggcacttattggtaaaaggcatttttacgaacgacactgataggattgatcactcaagaaatgttctcgaccctgaggtaggagtcttaacagacggacatcctccgtagatacgtgagaattaagggacgcatgtcgaaaacgcttggaatctactgtagtggcccaccttacgcttcttccaataactcccttcatagtccggcaacctcggtgggggtttcccttaggcctcggtgattgctagaacctccgcgcaaa
>19|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
ggagtggaaaattctgtagtccgttggcggcgaccgcaaaccagaataatatggtcacgttaggccctcgggccccttcatatgtacggagtcattgaattagcattatactaccgttacgcaagaccctatcccatccgcgactgtcaccactgctgtaaggttgcaaggctgtttcaatgtaaagtaggcgaattctgacgtgggctgataacgaatcccccgggttatctagtgcaagtgctatcc
>20|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 440 bp
atcttaaacagcccaatcggctcgccgaccaatttcccgcttcacagtacgcggaagaatctgcagatagaagtcagccctctcacgtcaataggaatgctgcccgtcatgtttaactactcaagttttaaggtgtcccttatcggttccaggatcatgtctgaaggaagatggtcgcaacgaaatctggagtggcatacatcgttcggtcgaagcataatctcagacgttatctataaagttagggcgctgtatggattgggattcaagctcgaagcctgttcctgccatacagcgccttagttaggatcacgcctgaaacgtcacgacggtgctaagcatcatggggcgtggcccggacgattatccatccgctacttgcgtatggtggtgtcacccaaaatatatgtcgcgaagagtgtccgtgtcatgctaccgag
>21|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 840 bp
cataactcgtgagtggccctgtacaagtcattgcatcacaatccttgcaatttgctcctttggccaagcgtacaagaccccggacccatacgctcccggctgataaactgctacagcatggtatatccggatgatgcccctgaaaactgcggaagtcaatttgttgatgaatccccgactttccgctgttcctgtggatggtcgaatgccaaatgaagagctgctccccccttctttaatatcaagcactacaaagataaagcctgtttggctgacggcgagccctcccctatcgtacgcaggatagatctggccaagtccgctgacgatggggtccacactgccagaagcgtagatctttgttgagtcggaccggaagagctaacctagctaagggtgtagagttttcaggagcttagagtcatgtcggattatggttggcgttacggacgggctccaaacgatcaaactctagtggccactttcatggccagaacggaaagagcggcgatgtctgccaagtaagaccttcactaccttccgttgattacagacgtcggtttgacagcttggggtcttatccggcgtttcagagaacttttggagcactgagcgcagacaccgacaagcttagctagacagctgaaccgtatcacttttgaaaccagagaaaacgcatagggtggttgaggtaccagaaggtgtggtttctaagttggaaaccacgtacatcactccttagatctccgaaagcgtcttcgcgtgttcggactccacatctatgcgtttactagcaagcggtttctgaccaatatgcctatgatatatcttaggtcggga
>22|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 234 bp
caccgcgaaagtgactcagttttcccggtcttatcacggtcgttgtcgtccagattccggttgttaactgcgggagctataacacttattccttactgcgacggctgatccactaagaacagttcatagagctcggctatataatttgaagacatagattccacggtacttgtagcccataaccgctgaggaggaacgtccaacggttcgcgcggagcatgtgacgcttaaagg
>23|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 917 bp
atcaagtgattacctggtaacccgccgctcttgcagtgttcaccctttgtgtcgtcttagtgtttgtacacgttaaggaaaagcgttagcttaaccattacgccccccaaagcccggtgtgtagttatctacatgccgtgtcaaagcggtgactaaatgtttatcaagttctgatgacaacgtgagctcttaaagccattgactagtataagcacggaacaatgataccaggcaagcttgaatataggataaggcctctaagctcgaagcggatcttacggaggtgtgaatcaacagcactcgagtagtacaccgtggatggttagtgaagttggtggtaaaagagtaaagggttctaacaccttaacaatgcgctacacttcaccatagccgagagtcagtatgtggtaccgttagttctttcaatcccaagagcgcataactgcttgccgccgcttagtttagggacattaatgtatatgatgaggggatgctcccttcattcggaccgaccccgacacatcgtatcctaatggctaaccgctcgcagccccctgcctgcatgcggtccgccgagcagtcgaccaagcactgtgaaagaatttgggaaatcgaacccagactaccggaacttaactcacgaccttcgatcttctgatcccagtttccatacttatatatactgcgcgaactgcagcggactttcctccggcccagcctatcgagctttgcgattgtattcgaggggcgtcggtatcttttatccaacagctgtcatcagttcggaccggggggataaaagcgccagactggatctggggtggtgtcaaccatgtgagtcaatcgtccccgagtgccgagggcctagggttcctacatggtgggtgctcctgtcgaaagaatcgagtgacgactcg
>24|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 676 bp
cacacggcatcgcaaagcgagctatccagagatgatacatgtggttgaaggtgattgcgtcaacatgggggttgctcagtttggttggtcaatcaacggtggcagaccatgcgataacgatgatggtaagactgtaaggtaagttaaatactctcgtctgccagttgggtcgtcaacgctgcagagacgccattcttcccagaaggtccgagctttctacagtgccgcggcgtcatgaccaaaggggtccaacctcgcagtaaaatgtctatgcttctggtttggaatgagaccgggccatcccgtgataaagagcttcatttatcagggaaagcgtcgcgtagctctagaatttatttatcttgagtcaaatgccatcatctaatgaatccactgagctggtaaggcctaggcaggcacggaggactttatagtccacgaattcgggcatccgcattatcttgttcgtccgcacttaacgactccatacccgaccctgttactctatcgagtacactacggttaaccgggcgtcattgtccacaggttcacagcaacattgggcgaagaggagtgctaactaagcgccatgccccattctaagtttacaacaaagtatttccaagcggacggtccgtgtttcagcctcatcttgcccccctggacattccgatgg
>25|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 870 bp
ctgatcaccaatagcttgcgcttaacacacgcgccttacaattatatgacgcccttgccaatgacagatagagccattaatcgtggaaaccaggcatttatacttgtccgatgtatcgattctcctctatctacagagcccggacatgcgaaatatcaaaattccatgtatactgaataaatacattgggcaagccgggctcatgcagcaatcccagcgttgccttacgcaaagatatcttacggagttgcctttagattaacagcacgtgttcaaaaacctagccaactctgtcggtctagggcggaacgaagtagccagagtcgccccacgcagttcacgattacagtaatccccttatggttggggcatcgggaaattaaccctaagatgcgccccttgagcgccgaaaagggatcagttcagagtttccccccattcattgcaaggcactgttcaggcgctaacatgaggcccaaaaactagctggttacttcctgcgtcgcgcaactgttcatgtgttctttccgtacctgtgccaaagtccatgttgaggtacacccttgggtgtgttagaaagtggcttgccctcatagctgctatgggaaatttgagttgcgaccgtcgggcctcagggcgccaggtttggctagtaggcggcgtcttgtgctgcgtcaactgcgaaatgatgtccggtaggcttttatgggtcgttgcggccatgcaagagcatgcggccggttgtcggttacagagtcttagatactgtcaaactcgtacacaataaagagaggtactaatgaatcatgggcagcgcgttcatagtatgtgaaacttggcaatcagtgcacggttggccccacggtccta
>26|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 751 bp
gggtgcgttatggggactaaagactgttactaccggtactccgccttatagagccgtcacgtattaatcagctatcaacagatactatcgtcacagccctccttctggcgaaggatctgagcatttgcaaagctataagttggtacgcaacggtagagggcttcgtagtcggggaaagggcttgcagtagtataggccgtaacttatctgttgcaacctcaaccgcacgaatcgattactctataactgccctcaatacagtatggttaccagtcaccttcacactgaagattaattcgcctacagaaggagaacatctaggtctccgtagaatagcagtcgtgacaacacgccgaaacttgaggcaagctcaggcgtgtgtagcgagctttcagcttaggcgggcattacctaattgttacggaccccccaaaaattgtcgactggtttcttctatgcgactataaaacaggaataggaaagtgggtgcatgcaacttgttcgtgtaccgttatgatcgattcctatgtgggagtttgcgcccacctcgtctgtgctgtcccggcgtactgcaccacgctgatttatcttgtagtaaggatggggtcaatacgagggctgaggcgtagagcccgacgggaaacacattcgtcacgccgcaaatcgcgtcgtcctcagacctcagcaagaccttttggtcagaatatggcggggctctaattgcctttacttccactccgtgaacttccgc
>27|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 574 bp
gtactgcaccttgcactgctatctacaatgccgagggtcgccctagtgctttgcatgtttggcctctacctacgagtctacgcgggcgtttttaagcaagctacgatcatcttgatccaagggtacgaggccccgcagaccaatggaggtcgtgaccaccctcgtgtatgcctcgcactaagcgagcattctggtatactgtctctctcctgtgataataacagtcggctcgatattcagttcacatgaaacagtatgttatataggtgggatggttataacacggaaaggtgaaaaagagtgcggaagttacttaggagtgccgtccttgatcaagcatgcgtagcaacaagcgcccgtaacaaccggatggaggttctgggtgaacaagggcgcccctacaggatatacaggacttgccctatggtccatttatagtatggtggtataccccggctcacctgtgaattagattgcgaaccaaataaaggatcatcgggttcacatttaggttagagccctcatacgttaacctgccggtacaccacttctttcgccgccgcatagtacatgc
>28|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 169 bp
agctccctaaacaacacccgcgtaaaaccttcagttatggtgccgactaaccctgtggatgtcttagcgctctcgttccgatgggtgctgatactagtaaatgagactcgagaccgagaacacgcaacggctacaacctggtcggttgttggggtttttataatcagtg
>29|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 408 bp
tgcagtgatgcatcgataagaccgcatagttacctccttacaggtgacgctaggctaattgggagtgctggcacttgtgccctacagtcaagcgctcacgcggtgttctcctcccgcaatcttagatattaggctctgtaccgcacgaaggatgaattttcttgactattggtccctgtttacgagggcttacctagagtgaggatgaacataaacaaggcctacttgacttaaggcttccaaatcacttgagggcaaatgactcctcaaacgcgagtgccagtactatccgtgagggaagaaaatctgccaaaaggccttggccgagatagattccgccgcccagcttacggggcatggtctataagttccgttttagcatgtactgtcaacaagcctgcgggatcc
>30|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 52 bp
caaagcgattcgggttaacgcacttaagagttcgacgtaggttagtcccctc
>31|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 581 bp
tgctctgacgtgtaagcgccttcgataacgtctttgcagcgccccacaaagtaaggaccggtctaacagggcttccgaatcaatagactgatagtaatgggatcctgaggctgggacccgacacacggcatattttactagaaacgctgatttaaactccaattatccttgacgcactgagccacagtcttagacgcagaatgtccgcaggagccctgtctttcccctaaatcattcgcggcatttgtttacgggttaagtcctgcggatcctagagtctgggccccgtacaaccaggaagagactgatactccgcgtattacggcccataagaacggtgggcctcgtttgtatttgactactgtacactcctgcctactgctgaacttaatgatgcgagatgaaagtcacagggggtgtagatcaagttgcacttaggtttcttccgatagattactatgcaagctatccacatgtgagaagctatagccacctctcttaacttctggtaagggcgcattgcggagcggcgagtacatatggtcttaatggacgccggtcgccgtccagatggagatagc
>32|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
gcggaactacctctctaagaccgcacaacaagtgtagtagatgaagatcacgcagagtgctcggcactgcatttttatacgtcgaatcagaaacgaggttcctcctctaggcttgttaaaaatccgggcgcgatgggctggtaatctgtggccatgggagcctcgccatttaaagattttggttaaggctcctctgttgtgtccatcacccttgaacgagcccgtacaaaccgtgtacgatgttgacac
>33|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 297 bp
gccctcgcgccagcttacttttagaaaacatcgaccggtaagagatacctgggtgagctgggcttcacgacatgttcttaaatcaatactctaaatctgctttgtagcatgcctcaagtaaaaaaatgtgctggttccgcacaggtgtgacgattaacgttgcgcccgtttgcgtcagtccagatcaccgatcttccacaccaccggtgggctgccggactgcaggtaatgactcctggctgcattctctgacataaaggttgaatagaacggcgtccttgagaaggttatggaacg
>34|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 573 bp
gcctaggggtcttgaccacagggagtacgagcattgatcattggagcaggtggctaatattgatagtggttagaccaccggcgcatcatcgtacgagcgcgggcgatacgtgtctttcaccggcgcactaatcttatcttacttctcaagccccgacagcatgtacgccaagtgttgttctgatgaaactttcgaaatagcaactgttagtcagttatagttggggagggcagtgaatacctcaaatacacccaagaaataacttcgaagcggcgcctatatcacacccctgtttcttatgactggtttgcgtgtgctaacagcaatcaagtacctgaccgtatgtccttgaagcttgaggatagtacccggatccagaggactgaaaaccgtgtctacgctgttctcacgccgatgtttgaaataatgagtgtagcgtctgccaaactggcttaagcactcagcgtgaggcgagattctatggccttgcgttttcgtttcgcgcgaacggtgacaatccagaaccccgaccttaaatatgcgacgtaaccctcctggccccgtccgagtgaa
>35|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 559 bp
gaaaaagtcgccccattcagttacaatcgtcttcagaagccagctcggttggggctatctgcggggtaatgcaacagggggctaccagacggtaaaccagggtcttgctattggtgttacgaaacaaaggagctatgcgacctcattagatcgagattactctcacaggcagctccggccatagcacaactaatttcgggtgtggagctcaccacaggaacatcttgtgcgtcctttgttatttaattgtgcattgtaatgcaccggaccccgggaacatacagccattatctgtgttgccgctcatccgttgtacttcttaatacaatcagaattgtactcaaccgattgccaagcacgtacgcgtcagatacacatccggagtcagtcctcgtcctgctttgactcatgccaaggagtgcgcttcgcgcgggtgaatctcgttatcgatttatagtatttatcttatcgcggaagaccacgctagtagactgggtaacgtcgcgattgtcccaaagccagagtgaagataggcgacatcctctgtgagaggggtacc
>36|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 187 bp
ctaagtccttatctatgatgcatctttcgttactgcgacaatatccgagacgagcagagttacacgccgaggtgtaaacgaatacgattgctatatgcaacgagttggttacacgcgtgaaggcgaatgtggatgctgcacttggagtcccattttaccggccgcacgtgctagctcactcaccttg
>37|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 549 bp
ttcatatggggatttggaatcgggtttgtgcggaatatgcccacgagactgcttatgtcaacgagacgacccattgtcacgttgtaaggccaccaataacacacaggtcttcgtttgctgtctcagggcaatcgcatcgacaacatcgtatggataccgttttttatcagcttacggcgcatcatactaataaggtgtttgagagggcgcagactcgaagcagtgtgatcttcccggttcgaagatgcaaaaacggtcctatttcgatccaaaactcagcgcactagtccaatgcttttttggagggttttgtagaacaatcgaggcgcggagcagcgaaatagaaaacgggccagtgaacgacggatccacacggaggtttcactcgaggacgtgtgccccaacaaccggttatctccttacttattcaagtgtgcctgcacctcgataagtctaaactccgcctatcccagcgtaggtcatagtcgtaactcccaacaggtgccctgcgacttgttcctcgccggtgctgcaagaaggtagtgttct
>38|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 916 bp
gtggcctaccataaatcaatttgggttaacgctctttgatctacgcactatgttgattcacttaccccttgtcaccgggcagaagagagccagtttaggtgtggttgtatttgccaaaccgcaaaccgcctaatgagctggatccggccatggaattaatcccgtcgtttgactcgaggtgttcaaagactgtgcaacacgacgtgcattcatcactagaacttaatctagaccaggccttgtggccaggagaggcgacgtgatattgccctatacacagataattatatacccctcgcgcgcaaaccatctcggtctctttccaaggtgccagcacgcgataactcgtatctgggctggatgtgcgtttcccttagcccactcccccttttaagtactagcgtactcgggttctacggagtgcatggagtttccacaaagggacgcaacataatttaaagaaccgagccttacgaggagcttttgcaggcttccgtcgctatccgtcgtcatggagtgaggctttgaggaacgagcacttgggactctatataccccggagtaagtatctacagccggggtctgacgccaaccatttgttactttgttgcgagggctactcccgctagtagtagaactgctgtcaggcaacgacactaattaagtggccttgacccgtacgacttgagaatcttcggttcaatattccccgtctcgaaaggctgcttcaagtgcgctacacattacatacaactaggcgggagggctccaaaccggcggagctacaaggagtctaatagtgcgaaaaaagggccgcgcgacaaatgagtctggtgtggcattcggaacgagtgggaacgatccgaatccgctttgacaattaaccgtcctaattaggatttcgtgaatagtagtg
>39|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 848 bp
accccggtcgctttggccggtcgtagccctaatcaattctgttcgtatcactaaagtaacggtttgaaatcctttgcaaacttgatctgggtatatgaaccggtatgcggggatagtggtaaataagtagtttacgagctgagcgtggattatcccagagaagttgccttaggtccagagcccgcacctacaatcactcgaggccggtcgagcgttgcgtggcaaggaaacccagccggtcaccctaccctcaaactcacgtcattgatccaatcatacatggcgtctctcacggtggtgttgtttgctgtttcttgcggcccgtttattcgtgaacacgacgcaagccctaccgacctcgctagccgatctagacgactgggtgggttacccttcccagaggagtgactatggatatgtagtccttataggcatccagggcaccggatgcactagtcacacccctgctcagatagcgccaaaaagtgaattcaagcgttcagctggacacccattaaacacgagtgctactgggcttacataatacgagagaagattggccgattgttgcccttagaacttatgtgaggtaagtctgagacgccgattgcggcctagacattagtaaaaataagataagaactactcccactgactcgttcgggcctcctagagctagggcccccctgagcatgttcagttatatcctacgggctagcgtaaggttttttcgtttatgcgaggcttgagacgcgacatacgagcattccgttgctggggcgatagaccacgatacgctcagaagagggaatactaaattgataaaatgctttcattgtctagcacct
>40|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 289 bp
agagcaaaagaaagtctgctccgcgtgacacacttgctcgttgtagtaactgcacgcgccgtctactcgacagggaccccccgtcggttcctctctatagcaatcgcggaagtggttccctgcctcccgcgcagaagttcaaactagtaatccttaatgacttgtggggggggagatcagtttcttccacaatggagtaaacttatgcgagaatcaagatcgcagaggccattttttgatgatactgtcagatatgtggttagccgtatcacgttaccgacgcagaatt
>41|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 642 bp
ctggggaatgaccgtaccgatctaattccccgtcgaaaaacttatgacgcgcagttgtccttatgcttgagacatgaatccttgccccatattggcgatcttggccaatgagatctgtcgaaagtactggaggccggtaaattgggggctctagaggtccgcccctgaaggactaacgtgtgtgtgtgtctacgtgtcgggttatcagcgtgttggacgatggccgtggattcaacgcatgctagagagctaatgatcctccgaagtcaaaagcctcagtgcttcgatttatgagcgcgtggcgagtacgtctagtgatactctaactactataaacaaggcctcgtcgcagaatccttcaatacattgggccccgggagataagtcggaccaggactaaattacacatgggggccctaaccctaggtcttaacggatggcttgataaagcacgcgctaatcttccctatcgtgcacatatctcttgctaccccctgctaaatcgctcgggccttggcctacacaatatgcaactggaagtgtggtttcgcaagggtataaataactgaactgtgaagttcccctgttacaaagccattagccgctaatgaacatagacctaacggactcgctccttgtgct
>42|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 993 bp
gcaagaagccaaaaaccttgcaggaggtcatttaagtttacccgcgcataagcagagacggacctctctgagatctcgcaccgcgcgcccggccggcactatcgatgctagactagggttggtgactagcccgtcaaaaccagcctaaacgcaaagattgtaggcgctagtccggaactgactgcttcgtgtcggtgggagcctagtatgtttccgggtctatgacccctaaaatcatagacgtgtcttaatagctatacctgacttactttgaagtacttgccacgacgagtttatgagatattagtattctcagccttgtgctcctcctacgaccgggatgagtcatctggtcaccttgatccgtacggaactatagatagtcacttcgaggcatgcgcgtttggacacctactgcttctaagtcatagcgctcgcgtaatgcagcctcgcatgttctttacacgacacgagggattttgattgttataggtgaacgtacagacaaaatcactgtttcagaatacttggcttgtacgatctccagtactccccgtgccggctcggcgaacgggataagacatccacggcattctgtagtggttgaccgggtttgacagactcccttatctggatggggcccgataacgatgagcatagaaccgttgtaagtctcgattgtcacccgaggacaaaattttctcatcctaggttcactcagcgtcgttagagcatcagagttccgtctttaggttactttaaagatcgaaagaaaccttcgtgctggtaggaagtctcatataagtagccagcgtggaccgaggaatagattgttatgttgcatgtacttctgggatcgtgtccagccaacttcaccgcggcacacgtcgatggacccaggaaatgcctcggggtcagaatgagccttgtgcggcccgactgctgaacgacgtataaaatagagcgtcgtggaccccatacaacgcacataac
>43|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 473 bp
ggttgtccaggcgcgagcaagtagctgactcgctaatcttaacgagtattgcttaggacttccaaatactccaagacgtcaatacgctttatctttgtgaagtcatcccggaccgagcgcttgggtcgtgatttaaaatcccctgtgatgtggctacaggtgcggcctatacagccgagaagaaggccgtctttaggcgtccaatgaaccgttacagggacacaccaaactgcgccaactgatcccacgggtcacggtacgctctaagaccagtcgggattctgacttaacatcgcagcatctgatcgagtggcttctccagcgagcctagggcattacaccgtgcgttcgcaaactctgtatgcttgtcggaaggtatagcttgagcccctttggttcatatcgttaatacttaagtaagtggggtcaatctttttgaactaatcaaatgactcactggcgaaaggcagacg
>44|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 272 bp
gtagaacttgttccccatggacaatgctagttccgttaatgccaggtattcatgtgccaagcgcctgcctggggaatacgagcctctctacaaacttacggccaccatgcttaaagattcggtgacttcactaatgacctatacaagtaatgcggaggacgctgtcgcttattgctctttgctaaggccagttatgtccgtcagtcaacgatacgctgcggcggtgggtgacggcactagaccggaagcctgatgacaagttcgaatcaata
>45|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 860 bp
aaaagcatcactctaacgacgctaccgtctgaatagatcaagattgctatcggttcgaccttgatcgcatgtgaacccgcccaaaaacccgtctcgacaaaagttacgtcgcatgggctgcgccaccggatagctcctagcttatcttataaatcaggtagagctacaacatggtgctatgacaactggagtgtcatcgctttggcgaaaccgtaaagggtgggaattgctgcattctcaactgggccgaactattccgcattcggctgctcacaaatcgtggaatgtgtccttgaacgtcctgcttaaccatggtcattgccacgaaggccctggtcggttcagaagtgtatcagacttacaagggtccgaggaggttccggcggggggagaacaagcatcgaacacgactcactgacctgtaggggtattacctatcactgtgacccacatctgaggtactggtccattccataaagatcgagtcgtcttcctaaactgggcactcatacgtacaggaccaaaaaagaggttggttggtgaccgtgccacgcctggcggtcagaatgagttaatgggtcgaataggcgatcttgataacaatagagattcacaacgtgggctcaagccgcttcctgcgaccactattagcgaactagggctatcgccacggaaaagtacttctaacatatacccctatggagtttcagtgtgaagccactgagcagtggcgaggttgtcgcgtcttttgttcaattgttccctgtactttaatgttcgtatcggatttgctttccgttgatagcgaatctctaccctgtcgctgtgtctagcatccgtccgcgaagccggtgacacat
>46|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 884 bp
aagcctctacaggctctgcggtttggctttacttaacggtgagtcaggaaaacattactgctacgttcaccgtgttcagagatagagagtacattagggaccaatcacaacgttcgccagggcaccgcctaatccgcgttgttagcaagagtacaggctctcgtatactttcagacccttcaatactagacgacaaattgcagcccggggtcatcggtcgactcagatacgtgctaacgagtaccaggtctaccgttgcaacgttggatgcgttatactcggcataaggcgatgccctttgacatactgcactacgctttggcgatagcgctacagttgatgaccgggctaactgcacgcgcgcgtagacgggagcccaattttttgaaattggcgacgaccgacttacgcacctatgcctcgcacgaccagtagctgtaagctctggtcgttggcattagattggcgaaccgctgaccacgatttaagccttccaaatcgttctactatacgagctcagcgtggcggtatgctagttgataaagtaaggacgttctcccgggtccagaagcccgatccacttttaaaagggctgatgcataaactaagactgtatgtctggttcaagtcttcagtaacttcagcctatgtttccaagtgacaacttggagaggggatgctgcggattctgatctaagctgttatatatctgttatcacctcgaaactatcactctggatgaccctcctatgtgcgctcagcgtagaccttccgctgtactttcataaacatagcatggagtgactcagaagagctttaaaggcgggagatcataggtcgcggtcgagcgaatgggaccgaggggaatgccaccaattcccgct
>47|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 888 bp
gcgccttgaagaggcgaggtctaaaggcaaaaatttagatccgccctatgagacggccgacgcggagaattccctaaccactattgtcctctgcatcgatatcaggaataggcttacctgcaatctcttatggtgatagactgtttgggagctgaacctgagacgcgcacgaaatttggaaggatcaaataggccccgcagtctctggtagacttctgccgagcggactagcttggctaaggtgtacaagcctaaatcgtttttcacatcaattttatagctgattatagaggaacgacgcgatcgtgcagagtgatggtcaaagggtcggtacgtcggatgcccagaaatatggtctgaggggtagcctgttcagaggcgcttaacttgctccttgctcacaggagcgatatgcgctagggttctggacgatcgaccatcattgtaacccatccaatccgtccttattgatggcccactcccgcatgctggtccgaaggcgatcccgatatcccgagcactagaattcgacacagtctgtaccgtgcctaattcttatcagaccctttatgcccgtctcggccttagagttaaatggactatctccacggaatgggcagtgcatcgctaccaagggtcgcccgatcccggggtttccacttcggatcatttttgtggatagtacatatcccacttcaacaagatagcaaaagtccaagacgcagtagagcacgtttctcaaacaacggaccatgcacggttcccggtaacccagtccagggaacaatttgtggttcttctttgaactagttgggagcaacagactcaggggctggccagtagtattgaaccaagcgttttttacaattactttgctggcgctaactg
>48|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 588 bp
catcaagatgggttacgtaggaccgagattcagtctctgggttagagccgacagcggggccgctacatagtacacggcgaggaatgcggggttgggctgaaccgtacacagtgggctagctgcggtacctgccaccggcatgcgtttaaatcctttcctttggcgaagccaactgccgacgtccgcaacagagactcgttttccgaccccgttactaaatcagctaactggcgcctgaatcctcttacgtcggatgttaattagtgtatagaatatcggagggttgagtgcgacgcgcttcctgttctccgctacttcttgtattatgatttggtcaaatacagtcgacaatagtgctcgacaggatataacgctatggcaccccatagtatcagctaaacgttcatatcctagtagcttagaaagaaatttaatatgcagtggagcctggaaccttacttattgtcggctcatcccgcaatactcgcaaataatcacgcatggtgccggacggtacgggccacgtcaattaggtaaacgaaacacgttacgtggactgctcacccaaccttgagggactgtctactt
>49|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 626 bp
taacctcagtctcgttcccccctcggtagttcggacccttattcgcttatctcacattcatcactgtagaccaaggaccgggcatacttgcggatatctaccaggactaggcacttagggatacgctgttgaatacgggtttcgtcccgtgtactcaagtgtagtttaagataggtacgagtgctagtacatcgtacaatttacaactgacttaaacgagagtttattatgtcttgttcacttgttgacacgcctgggaaaataataaaaggcaacgtctaatctcagacccgttgattaactaagcagcgtgacgtggagtcatacctgctatatttgggaggtgggaagtattggtgaaccgagcccctcctagccgtggcggtaatgacattaagaaggcgcagttagtcagcactcgaggcaggtgcgcctctgcacgtctgctgatatcgtcggaacgagttaacgctcccgcccacccatcagtcagggaccactttcgacacctagttcgagatttctcctttcggtaaaatcgggctcaattaaggcttgggtaccccggccagggaatatgcacatgagggaactatgagactgcacctaccccgcacggatggagg
>50|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 214 bp
taactgtcggtcactgctcatcccgactagttcggctcactagacttactcgcggaagcgagaagtaggacgtcgtgtaatactccaacgtcgttacgcaatgttgtaaaacttcatcgcattccgtgcatggcctaaacgtgcagcattatataacgctctttggtcttaatatccatcgcgggagtaacgcgaaggggagacgtgtgcctga
\ No newline at end of file
diff --git a/read_sequencer_package/modules.py b/read_sequencer_package/modules.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..ca84a645b8a5f88f1d3c083d5d489917b3b90adb 100644
--- a/read_sequencer_package/modules.py
+++ b/read_sequencer_package/modules.py
@@ -0,0 +1,69 @@
+
+def read_in_fasta(file_path):
+ '''
+ This function reads in FASTA files
+
+ argument is file_path
+
+ it returns a dictionary with the sequences
+
+ '''
+ sequences = {}
+ f = open(file_path)
+ for line in f:
+ if line[0] == '>':
+ defline = line.strip()
+ defline = defline.replace('>', '')
+ else:
+ if defline not in sequences:
+ sequences[defline] = ''
+ sequences[defline] += line.strip()
+ f.close()
+ return sequences
+
+def read_sequence(seq, read_length, padding_probabilities=None):
+ '''
+ This function reads sequences
+ arguments: seq is a list of sequences
+ padding_probabilities is a number??
+
+ returns sequenced element
+
+ '''
+ from random import choice
+ bases = ["A", "T", "C", "G"]
+ sequenced = ''
+ if read_length >= len(seq):
+ for nt in range(len(seq)):
+ sequenced += seq[nt]
+ for nt in range(len(seq),read_length):
+ sequenced += choice(bases)
+ else:
+ for nt in range(read_length):
+ sequenced += seq[nt]
+
+ return sequenced
+
+def simulate_sequencing(sequences, read_length):
+ results = {}
+ for index, key in enumerate(sequences):
+ results[key] = read_sequence(sequences[key],read_length=read_length)
+
+ return results
+
+def write_fasta(sequences, file_path):
+ """
+ Takes a dictionary and writes it to a fasta file
+ Must specify the filename when caling the function
+ """
+ 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")
+
+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)
diff --git a/read_sequencer_package/read_in_FASTA.py b/read_sequencer_package/read_in_FASTA.py
deleted file mode 100644
index 85fae3817dfdc836a811ec771327a13215fe11b3..0000000000000000000000000000000000000000
--- a/read_sequencer_package/read_in_FASTA.py
+++ /dev/null
@@ -1,26 +0,0 @@
-'''
-This function reads in FASTA files
-
-argument is file_path
-
-it returns a dictionary with the sequences
-
-
-'''
-
-
-import sys
-
-def read_in_fasta(file_path):
- sequences = {}
- f = open(file_path)
- for line in f:
- if line[0] == '>':
- defline = line.strip()
- defline = defline.replace('>', '')
- else:
- if defline not in sequences:
- sequences[defline] = ''
- sequences[defline] += line.strip()
- return sequences
-
diff --git a/read_sequencer_package/read_sequence.py b/read_sequencer_package/read_sequence.py
deleted file mode 100644
index 45a5c6a6a2f9f4a8c73ba95b8c9d5d458fcc97df..0000000000000000000000000000000000000000
--- a/read_sequencer_package/read_sequence.py
+++ /dev/null
@@ -1,31 +0,0 @@
-'''
-This function reads sequences
-arguments: seq is a list of sequences
-padding_probabilities is a number??
-
-returns sequenced element
-
-'''
-
-import random
-
-
-
-def read_sequence(seq, padding_probabilities, read_length):
- reading_element = random.choice(seq)
-
- bases =["A", "T", "C", "G"]
-
- if read_length > len(reading_element):
- for nt in [0:len(reading_element)]:
- sequenced += reading_element[nt]
-
- for nt2 in [len(reading_element):read_length]:
- sequenced += random.choice(bases)
-
- else:
- for nt in [0:read_length]
- sequenced += reading_element[nt]
-
-
- return sequenced
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 528670cb0aba646f293aeb91aedbcdcc5d617d55..1102b5a453b8bd5c032792a7a3058446e70d6fb8 100644
--- a/setup.py
+++ b/setup.py
@@ -1,20 +1,17 @@
- from setuptools import setup
+from setuptools import setup
- setup(
- name='awesome_read_sequencer',
- version='0.1.0',
- author='An Awesome Coder',
- author_email='aac@example.com',
- packages=['random', 'sys'],
- scripts=['read_in_FASTA.py','read_sequence.py']
- license='LICENSE.txt',
- description='An awesome package that simulates sequencing of a FASTA file.',
- long_description=open('README.md').read(),
- install_requires=[
- "random",
- "sys"
- ],
- entry_points = {
- 'console_scripts': ['read_sequencer_package/cli.py:parser'],
+setup(
+ name='awesome_read_sequencer',
+ version='0.1.0',
+ author='An Awesome Coder',
+ author_email='aac@example.com',
+ packages=['random'],
+ scripts=['cli.py', 'modules.py'],
+ license='LICENSE.txt',
+ description='An awesome package that simulates sequencing from sequences specified by a FASTA file.',
+ long_description=open('README.md').read(),
+ install_requires=['random', 'sys'],
+ entry_points={
+ 'console_scripts': ['read_sequencer=read_sequencer_package/cli.py:main']
}
-)
\ No newline at end of file
+)