diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index e67a40ec0cbb5aa7e77e9607e08a517dc1187296..0000000000000000000000000000000000000000
--- a/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.DS_Store
-.idea/
-__pycache__/
diff --git a/LICENSE.txt b/LICENSE.txt
deleted file mode 100644
index 9ae3ad477bffeaa0ed46b1887c9cdde30ce6b73f..0000000000000000000000000000000000000000
--- a/LICENSE.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2022 Clara Serger, Michael Sandholzer and Christoph Harmel
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
\ No newline at end of file
diff --git a/README.md b/README.md
deleted file mode 100644
index 3003dfb80d3d09bd805b71f5eb1b1c13bbfea12d..0000000000000000000000000000000000000000
--- a/README.md
+++ /dev/null
@@ -1,29 +0,0 @@
-# Read Sequencer
-
-## Overview
-
-Read Sequencer is a test python package to simulate sequencing.
-It reads fasta files, simulate sequencing with specified read length and writes the resulting sequences into a new fasta file.
-
-
-## Installation from PyPI
-
-Read Sequencer requires Python 3.9 or later.
-
-Install Read Sequencer from PyPI using:
-
-```
-pip install -i https://test.pypi.org/simple/ read-sequencer==0.1.1
-```
-
-## Usage
-
-```
-read_sequencer --input_file_path --output_file_path --read_length
-```
-## Contributors and Contact Information
-
-Christoph Harmel - christoph.harmel@unibas.ch
-Michael Sandholzer - michael.sandholzer@unibas.ch
-Clara Serger - c.serger@unibas.ch
-
diff --git a/build/lib/read_sequencer_package/__init__.py b/build/lib/read_sequencer_package/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/build/lib/read_sequencer_package/cli.py b/build/lib/read_sequencer_package/cli.py
deleted file mode 100644
index e786d78de5391ea2b035c058f4de2cd16162a4d6..0000000000000000000000000000000000000000
--- a/build/lib/read_sequencer_package/cli.py
+++ /dev/null
@@ -1,23 +0,0 @@
-import argparse
-from modules import read_sequencer as rs
-
-parser = argparse.ArgumentParser(prog='read_sequencer',
- 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',
- help='path to FASTA file')
-parser.add_argument('--read_length',
- help='read length for sequencing',
- type=int)
-
-args = parser.parse_args()
-
-def main():
- 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/build/lib/read_sequencer_package/modules.py b/build/lib/read_sequencer_package/modules.py
deleted file mode 100644
index 39a686616817f6b496328d460fe06931f9670da8..0000000000000000000000000000000000000000
--- a/build/lib/read_sequencer_package/modules.py
+++ /dev/null
@@ -1,148 +0,0 @@
-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):
- '''
- This function reads in FASTA files.
-
- Args:
- file_path (str): A file path directing to the fasta file.
-
- Returns:
- Dict: It returns a dictionary with 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):
- '''
- 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.
-
- Args:
- seq (str): the sequence to read
- read_length (int): length of reads
-
- Returns:
- str: 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):
- """
- Simulates sequencing.
-
- Args:
- sequences (dict): Dictionary of sequences to sequence.
- read_length (int): length of reads
-
- Returns:
- dict: of n sequences as values
- """
- results = {}
- for index, key in enumerate(sequences):
- results[key] = read_sequence(sequences[key], read_length=read_length)
-
- return results
-
-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:
- dict: 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
-
-def write_fasta(sequences, file_path):
- """
- Takes a dictionary and writes it to a fasta file.
- Must specify the filename when calling the function.
-
- Args:
- sequences (dict): Dictionary of sequence.
- file_path (str): A file path directing to the output folder.
-
- """
- 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")
-
-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)
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diff --git a/read_sequencer.egg-info/PKG-INFO b/read_sequencer.egg-info/PKG-INFO
deleted file mode 100644
index ed2a2f723157a60010ad224e55406bda28f82255..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/PKG-INFO
+++ /dev/null
@@ -1,9 +0,0 @@
-Metadata-Version: 2.1
-Name: read-sequencer
-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
-Author-email: christoph.harmel@unibas.ch
-License: MIT
-License-File: LICENSE.txt
diff --git a/read_sequencer.egg-info/SOURCES.txt b/read_sequencer.egg-info/SOURCES.txt
deleted file mode 100644
index 9b093f4ab2fab7288a29384742947a5405d68517..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/SOURCES.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-LICENSE.txt
-README.md
-setup.py
-read_sequencer.egg-info/PKG-INFO
-read_sequencer.egg-info/SOURCES.txt
-read_sequencer.egg-info/dependency_links.txt
-read_sequencer.egg-info/entry_points.txt
-read_sequencer.egg-info/requires.txt
-read_sequencer.egg-info/top_level.txt
-read_sequencer_package/__init__.py
-read_sequencer_package/cli.py
-read_sequencer_package/modules.py
\ No newline at end of file
diff --git a/read_sequencer.egg-info/dependency_links.txt b/read_sequencer.egg-info/dependency_links.txt
deleted file mode 100644
index 8b137891791fe96927ad78e64b0aad7bded08bdc..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/dependency_links.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/read_sequencer.egg-info/entry_points.txt b/read_sequencer.egg-info/entry_points.txt
deleted file mode 100644
index 569e8154320e35d343a621996abf05109990fec6..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/entry_points.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-[console_scripts]
-read_sequencer = read_sequencer_package.cli:main
diff --git a/read_sequencer.egg-info/requires.txt b/read_sequencer.egg-info/requires.txt
deleted file mode 100644
index d9ca6c64cbd4a8ce3229966dd400911a7f626665..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/requires.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-random
-textwrap
-argparse
diff --git a/read_sequencer.egg-info/top_level.txt b/read_sequencer.egg-info/top_level.txt
deleted file mode 100644
index a5c49290c04dc99c11fd0696381a1287c34af400..0000000000000000000000000000000000000000
--- a/read_sequencer.egg-info/top_level.txt
+++ /dev/null
@@ -1 +0,0 @@
-read_sequencer_package
diff --git a/read_sequencer_package/__init__.py b/read_sequencer_package/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/read_sequencer_package/cli.py b/read_sequencer_package/cli.py
deleted file mode 100644
index 9a68267c115d328afa32e582d8c03e4aede2a076..0000000000000000000000000000000000000000
--- a/read_sequencer_package/cli.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import argparse
-from modules import ReadSequencer
-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',
- 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',
- 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("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("Read sequencer finished.")
-
-if __name__ == '__main__':
- logging.basicConfig(
- format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
- level=logging.INFO)
- LOG = logging.getLogger(__name__)
- 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
deleted file mode 100644
index 12e41cdac4403ac3c51f4f76553889346ab56bdf..0000000000000000000000000000000000000000
--- a/read_sequencer_package/fasta_testfile/50_seqs_50_1000_bp.fasta
+++ /dev/null
@@ -1 +0,0 @@
->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/fasta_testfile/result.fasta b/read_sequencer_package/fasta_testfile/result.fasta
deleted file mode 100644
index 32258d65e587dd9e7501d585c137d799103c60f8..0000000000000000000000000000000000000000
--- a/read_sequencer_package/fasta_testfile/result.fasta
+++ /dev/null
@@ -1,200 +0,0 @@
-0: length 103 nt
-ACGCCCTATGTCAGAGTGGTGTTAGTGCACAATTCATTCCGATATGCGAA
-1: length 35 nt
-ATAACGAGCGCGAGCCCTTAACGGGCAGGACTGCCGACTCACACCTTAAT
-2: length 61 nt
-GGTCTCATAAGCACTTCGGGTACATCCTCCTAAATGGGCCGCGACTTAGG
-3: length 54 nt
-TAGGTCTCGGATACGAGATATAACCGTAGCATGGGAGTGACACCCATGCC
-4: length 64 nt
-TCTGCGATACCCAATTTAGGGCATGGCATAAGGCCCGGCGGGTATTTCCG
-5: length 85 nt
-TTGTTAAGCGTGTTGGTAGCGCCCCCAAATTGTCCCAACTGGGCCACACC
-6: length 53 nt
-ATAGTACAAGTTAGACCTCATGCATTGAGCTGCCCGGTTCGGACCTTAAT
-7: length 27 nt
-TAAAATATTAAGGATAGCCGGAACGCGCTGGCGACTGACGACACTACACG
-8: length 25 nt
-TAGATTCCAGGGAATGACGTCACACCGTTCCGTATATCAGCGGCGCGGAA
-9: length 52 nt
-GGTGCACCTATTAACAGAGTGACTTTGGGGGAATCACTTATTCGCATATA
-10: length 41 nt
-AACGACAAGCTGAACGAGCTCTGGCGGCTACGCAGTGTTCGCGCAAGCGA
-11: length 106 nt
-GTAATAAACTAAACATCAGCTGAGGCGTCCGACCACTGCATCTTTTGTTG
-12: length 5 nt
-GTAATATGGTATAGCTCGACCCTCGTACAACGGGGGTCAGACAGCGTTGC
-13: length 49 nt
-TTACTTTGCACGCATGCATGGAGGCACCATGAAAGACGGGAAGCGGCTAA
-14: length 22 nt
-GCAAGGGGTTTGAGGGAGCAACGTAAGATCAGAGATAACAGTCTCAAGAG
-15: length 109 nt
-AATTGAAGTCAGCAAAGAATTGGGATTGCTGGAAGCAACACGGACACGTT
-16: length 43 nt
-GAACCATTCTAAACAGCACCACCCGCATCCCGCTTTGCGCAGCAGCCACT
-17: length 85 nt
-ATGTCTCACAGGGGAGGTCTCCAGGCTTCTACCAAGTTCCCAATTCCATG
-18: length 16 nt
-ATCTCATCAATTATGTTGTACACCTGCTCGTTCTAACTTGCAGACTGCAT
-19: length 52 nt
-GAGTATCGCAGTATACTGTTGGCGGACATTCCAGAATATTGGTATTCAGC
-20: length 2 nt
-ATATAGCTACCCCAGATTGTCTTAACGAGTCCCGCACCCCCCACCAAGAT
-21: length 13 nt
-GTATTTACCTGCCCACTAGTACAAGTCCCCGAACCTTAGCAATCCTAAGT
-22: length 64 nt
-TGGCCGTTTCAGAAGGATTCCTGCCCCTGTGATGAGTCACGTGGAGACAG
-23: length 59 nt
-CGAGGAGAGCTGTAAAATACTGCTGCCTGCTACATTGGGGCTTGGGTCTC
-24: length 82 nt
-GCACAGTAGCGAGTGACTCGGTTACTATGTGTTGCTGACTTTATATGTGC
-25: length 6 nt
-GAGTAAAGCTGAAACACCGAACCGGCAGTTAGAGCTAGTGGATTTTCTTA
-26: length 87 nt
-AGACATTTTCGGAACCAATGATCTTGTTGGAGTTGAGAGGCCGAACCAGG
-27: length 136 nt
-AACACGGTAATATCAGGTCGGCCTTAGTCACTTCGGAATTGGAGTTAGTA
-28: length 68 nt
-CACCGGTAGCTGAATGTAACGAATCTACGTTGACACGGTTAAAGGGATAT
-29: length 84 nt
-AGATTGTCATGGACTGACGGAGAACACCGTGCTTAAAGTGGAATAATGTG
-30: length 51 nt
-CGGCAAGGAGGAGGCTACTGACCAATCAGACAAACGTTCATGGCTAGAGA
-31: length 51 nt
-AGCAGCCGCTCAACTGTGACGTCGGCTGAGTCTACCAGCCCTCAGACTAC
-32: length 73 nt
-TCCGATCTTATAGTAGTGATCCTGATGGAACAATAACTGACCCAGTAAAG
-33: length 58 nt
-ACGTTTTATTGTACCTAGGTGTGGCACCATGAAAGGCAGGAGGCCCACCG
-34: length 28 nt
-AATCCGCAATCGTGCTACGCATTTTCCAGACAATATTTCGAGGTTACCGC
-35: length 13 nt
-AACACGAGGCCCTCTCGACGCTGCTATTTAACAGCGCGTGCCTATTGAAA
-36: length 2 nt
-ATACCGAAACTTACTAGTTGTGACAGCGGATTCCAAACTGCGGGTGAATA
-37: length 71 nt
-GTGAGGAGTACTCGGCACCGGGAACGTAGTAATGTGCTCTGATCCACTCT
-38: length 46 nt
-CGAACGTAAATAAGTCTGCTGCTGCCTCAGCAGAGGGATGGGAGGGGTCT
-39: length 48 nt
-CGCAAGAGTGTCGAGCTGGCAGACGCGTATTGCCTTTATATCCGTGAAAC
-40: length 63 nt
-TGACAAACATAAGTTTGTCGCCCGTTTCCACATAGTAGAATTCATTAGAA
-41: length 11 nt
-AGAAATAGTACGTAGTGTTGGCTGTGAATATTCGGAGATAAGGACTCATT
-42: length 68 nt
-GGTTCACAAATTGTCATAGATCATCGTGGTACGACGGGCGATCTTATTTC
-43: length 7 nt
-CGAGCGTGATGACGTAATGGAGTGAATAAGGAGTGCGAAATGGTGCGTTT
-44: length 84 nt
-TGGGACGATCATTCCCCCTGACCTTACGTACAATGCAATTGCGAGTGGCT
-45: length 23 nt
-TTGTACTTACGGCTTAAATTGCACAGAAGGGGTTCTCCGGAAGATAACTA
-46: length 58 nt
-GGCCCTTCGGTGCAGTCGGCCTAGGTATCAAGCTCGCCTGCCCGTGTTAT
-47: length 50 nt
-TATCGTGGTTATGTGCGGACCGCCTGATATTACAGCTGATGTGAGGGCAA
-48: length 63 nt
-TCTGCTAGGGATCCACTCCTGGGTCATTATTAAGCACTTACGGCCTGAGA
-49: length 48 nt
-GGAGAATTCGCGGCATAAGATCTCCATACGGGTAGTATGTGCCACTATTA
-50: length 64 nt
-AATGCGTACGGCCCAAAAACCTTCAGGATTACCATGAACCCGTAACTCAA
-51: length 41 nt
-AGTCATATAATGATTGAGTTCCCTCAACCCTCCGGACGTAAACACTCCGG
-52: length 44 nt
-TCCAGATGGCCTGGCAATCAGGTGTTGACGGGAACCGCACCCCTGCTGCT
-53: length 62 nt
-AGGTTGTCTGAATCACTCGGGAGACTTCCCCGCACGATATCGGCACCTGA
-54: length 73 nt
-CCGTACGGAACATCCTGCAGCTTCGCCCGGTCGAGAAGAAGGTAGAGATA
-55: length 39 nt
-TGCGCGGCGGACTCTGTCATTTATGACCTGCTTGAACGATGAGTGGGCCA
-56: length 88 nt
-CGATCCATAGGGCACGCTAGTTTGCATTTTAAGGAGTGCCAATTACGAGG
-57: length 117 nt
-TATTGCGTCCGTTGCCTGCTCCATCCGTTGCACTATGCCATAAGGCAACA
-58: length 67 nt
-TTAACGCACGATCAACGGTTCATAATCTGCGGTGATCCCAGAGCTCTACA
-59: length 84 nt
-CTGACCCTCGATGTGTTTAATAGTTGTATTTCGGCCCCAGTAGGCTCGAC
-60: length 71 nt
-CTGTCAGATGCGCATGTTCGTGGTCCATTGTCAGCCAAATTAAAGGTTGC
-61: length 102 nt
-TACATGCTCATATGAACTGACATTGAGTGGAAGGTAGCGACCGCGAGGTT
-62: length 66 nt
-ACATGATCTTTGTCGAATACTCAAAATGCACAGTGCCTAACTATTTGGGT
-63: length 22 nt
-GTCACGACACGCATCTACACTAAACAGCACCACATGTTAGAGATGAGATC
-64: length 46 nt
-CGTGGTCGTGAAGACCCACTATATTAGCAAGAGTCGCGATAGATGGGTGT
-65: length 78 nt
-CTAGGTAATTTTGAGAGACACCCCGACGCACGGATGTTCCGTACAAAGAT
-66: length 32 nt
-CAGTCTGAATGTATCAACTAAGAGAATCGTACGAAAATAGACCTAATCGA
-67: length 42 nt
-GCTCCGCACACTAGATAGCTGATGCCCACATACTCATTCATTATTCGATG
-68: length 49 nt
-GTCTGAACCAGACACGCACTACGGCTAGCACCTATCCTTATCCTAAAACG
-69: length 41 nt
-GAGTTACGACCGGACGGGTTGTTAGGTCACCCCGGAATCAGACGATTTAC
-70: length 29 nt
-GTAGGCCAACGCGAACTACTCCTCCCGCCCACAGTCTAGACTAAGCGTTG
-71: length 94 nt
-GGTTTAGACTGTCTGCAACTATGTTACTGGATATACCTAATGACAGGGGT
-72: length 48 nt
-TAAGAATGTTATTGGGCGGTAGCTTACTCTATTGGAATTGAGAAAATGTA
-73: length 63 nt
-CTAGTATGTTTTATTGGATGCTTGAGGTAGGAATAATCACATCGGGCCGA
-74: length 70 nt
-ACAAACCTCCTCCCCGGCGACGGGCAACGCCCGCATTGCAACATGCAAGA
-75: length 58 nt
-GGCTCCATTTCGCTACCCTCTCCCCTAAATCAGGTCCGCGGAGTTGTCGT
-76: length 98 nt
-ACATACCTATGCCTCAGATCGGTTCGGCTCTTGAGGCGACACCCGTGATA
-77: length 34 nt
-TTAGAAAGGAACTCATTTTAAGCAAGTTATGCCAGGTTAGCCCGCCCTGG
-78: length 48 nt
-AAGGCTCGCCGTGACCAGTAGTGCGCAACCTTTCAAGCCGTGTAATATTT
-79: length 51 nt
-CCTTAAGGGTGGTTTGCACCGTAAAGACCCTCTCTTCCACTTTCCCCGAA
-80: length 30 nt
-GCCTCGACGTGCCGGACGATGGGCGCTGATCGAAAGTCCATTGTCCCCCT
-81: length 14 nt
-AGGGCAGTGTACACACACGGCAAGGGTTGCGATGGGTAGAGGCTAAGACG
-82: length 39 nt
-AATGGGACTTAGTAAACAGGCTGGCCGCCTAGACTGTGTGTGAATGCCCA
-83: length 29 nt
-AGCTTGGACTTAGAGAAAATCAGTCTACAAGACATAGGCTTTAAAGAGGA
-84: length 15 nt
-ACGGAAAGTAAGTCTCTCGTCCCTGGTTAAAGGGTCAGTCCCTCCCACCT
-85: length 20 nt
-CCCAGAGCAAACTGGACCTCCCACCGGCAGATCATCGTTTATTATTATAC
-86: length 64 nt
-CGTGGCCAGTACATGCTGATGATCCCTATTACAGACCTCGCGTGTTGAGA
-87: length 52 nt
-GTTAGGCTGTACTGAATACCATGAGCATGTGGGTAGGTTGTACTGGAACC
-88: length 60 nt
-CGCCGGGCTCCCCGAAGTATAGAGCCAGCGGTTAAATAACTTATCTGATC
-89: length 32 nt
-CTTGTACGTCGAGTATGAGAGGGGTTACACTTTCTGCTTGCTAAGTTCAG
-90: length 14 nt
-AAACAGATTAATAACGTAATACCCCCGCTCTACGCCCCTGCATTACGGTT
-91: length 21 nt
-GTAGTTCGTAGCAGGGGATTGTCATAAATCAGCGCCTGATGGGAAGCGTT
-92: length 47 nt
-TGCCCAGATGTAACACATCCCGGCCCATTCTGGTAACTCCGTTTCTGGGT
-93: length 47 nt
-AATTAAGGGGTTGTCAAACCGGCCACTTTTGAACAATGGGCTTCGCCGCC
-94: length 42 nt
-TTCAACCTTTACGATGCAAACATAGACAAACTTGGACGTATTCGGACCCT
-95: length 35 nt
-GGCGCTTAGTGGAATGCCCCCCCGTATGCAGCATCGAGTATTCCGTAGCG
-96: length 54 nt
-TTGCTGATCTTTCGAATTTGGATCTGGGATTTTGCCAGATAGCGCCCGTA
-97: length 34 nt
-TACGTAGATATTTTCAGGAGGCACTGAACAGCCCAGAGCCTCCATCGGGC
-98: length 15 nt
-ATTGCGCAGGTATGGCTCAGAGACACAGTATACTATTACCTTCCCGCAAC
-99: length 42 nt
-CGATCTGGCATCGGCATCCGAGTAGCCCCTACGTATGGCTTTGCCCAACA
diff --git a/read_sequencer_package/modules.py b/read_sequencer_package/modules.py
deleted file mode 100644
index f92458982cf1d57721279b44344fad2f262f80ee..0000000000000000000000000000000000000000
--- a/read_sequencer_package/modules.py
+++ /dev/null
@@ -1,130 +0,0 @@
-import logging
-LOG = logging.getLogger(__name__)
-
-def read_in_fasta(file_path: str) -> dict[str,str]:
- """
- This function reads in FASTA files.
-
- Args:
- file_path (str): A file path directing to the fasta file.
-
- Returns:
- Dict: It returns a dictionary with sequences.
- """
- LOG.info("Reading in FASTA files from destination.")
- sequences: dict[str,str] = {}
- f = open(file_path)
- for line in f:
- if line[0] == '>':
- def_line = line.strip()
- def_line = def_line.replace('>', '')
- else:
- if def_line not in sequences:
- sequences[def_line] = ''
- sequences[def_line] += line.strip()
- f.close()
- return sequences
-
-def read_sequence(seq:str, read_length:int) -> str:
- """
- This function reads a sequence of a specific read length and adds additional nucleotides if the sequence is
- smaller than the requested length or cuts the sequence if its longer.
-
- Args:
- seq (str): the sequence to read
- read_length (int): length of reads
-
- Returns:
- str: returns sequenced element
-
- """
- from random import choice
- bases: list[str] = ["A", "T", "C", "G"]
- sequenced: str = ''
- 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: dict[str,str], read_length: int) -> dict[str,str]:
- """
- Simulates sequencing.
-
- Args:
- sequences (dict): Dictionary of sequences to sequence.
- read_length (int): length of reads
-
- Returns:
- dict: of n sequences as values
- """
- LOG.info("Sequencing in progress....")
- results: dict[str,str] = {}
- for index, key in enumerate(sequences):
- results[key] = read_sequence(sequences[key], read_length=read_length)
- LOG.info("Sequencing was successfully executed.")
- return results
-
-def generate_sequences(n: int, mean: int, sd: int) -> dict[str,str]:
- """
- 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:
- dict: of n sequences
- """
- from random import choice, gauss
- LOG.info("Generating random sequences.")
- sequences: dict[str,str] = {}
- for i in range(n):
- seq: str = ""
- bases: list[str] = ["A", "T", "C", "G"]
- for nt in range(abs(round(gauss(mean, sd)))):
- seq = seq + choice(bases)
- key: str = str(i) + ': length ' + str(len(seq)) + ' nt'
- sequences[key] = seq
- return sequences
-
-def write_fasta(sequences: dict[str,str], file_path: str):
- """
- Takes a dictionary and writes it to a fasta file.
- Must specify the filename when calling the function.
-
- Args:
- sequences (dict): Dictionary of sequence.
- 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")
-
-class ReadSequencer:
- def __init__(self):
- self.sequences: dict[str,str] = {}
- self.reads: dict[str,str] = {}
-
- def add_random_sequences(self, n: int, mean: int, sd: int):
- self.sequences: dict[str,str] = generate_sequences(n, mean, sd)
-
- def read_fasta(self, input_file):
- self.sequences: dict[str,str] = read_in_fasta(input_file)
-
- def run_sequencing(self, read_length: int):
- self.reads: dict[str,str] = simulate_sequencing(self.sequences, read_length)
-
- def write_fasta(self, output_file_path: str):
- write_fasta(self.reads, output_file_path)
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 905f8ee96fc23a232cf669563da1389e1228c9e5..0000000000000000000000000000000000000000
--- a/setup.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from setuptools import setup, find_packages
-
-setup(
- name='read_sequencer',
- 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','logging'],
- entry_points={'console_scripts': ['read_sequencer=read_sequencer_package.cli:main']}
-)