diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index fe236d6d40038e6d13d64badc3a9c2370d9cdde1..0000000000000000000000000000000000000000
--- a/.gitignore
+++ /dev/null
@@ -1,56 +0,0 @@
-# Created by https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode
-# Edit at https://www.toptal.com/developers/gitignore?templates=macos,visualstudiocode
-
-### macOS ###
-# General
-.DS_Store
-.AppleDouble
-.LSOverride
-
-# Icon must end with two \r
-Icon
-
-
-# Thumbnails
-._*
-
-# Files that might appear in the root of a volume
-.DocumentRevisions-V100
-.fseventsd
-.Spotlight-V100
-.TemporaryItems
-.Trashes
-.VolumeIcon.icns
-.com.apple.timemachine.donotpresent
-
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
-
-### macOS Patch ###
-# iCloud generated files
-*.icloud
-
-### VisualStudioCode ###
-.vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
-!.vscode/*.code-snippets
-
-# Local History for Visual Studio Code
-.history/
-
-# Built Visual Studio Code Extensions
-*.vsix
-
-### VisualStudioCode Patch ###
-# Ignore all local history of files
-.history
-.ionide
-
-# End of https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode
\ No newline at end of file
diff --git a/Images/.gitkeep b/Images/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Images/git_sunho.png b/Images/git_sunho.png
deleted file mode 100644
index fd10c600ac93b038db96236a6dc1b9bb62ba9ec6..0000000000000000000000000000000000000000
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diff --git a/Images/git_sunho2.png b/Images/git_sunho2.png
deleted file mode 100644
index 8b70717c0ef12171dbcabf31a034775e65ca4a37..0000000000000000000000000000000000000000
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diff --git a/Images/markdown_sunho.png b/Images/markdown_sunho.png
deleted file mode 100644
index a9a594b9e2c69cd7d1fc6ab229a2b141d0c466d7..0000000000000000000000000000000000000000
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diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index edb874900e3f120cb97930894f9a0c54cbb340b1..0000000000000000000000000000000000000000
--- a/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2022 zavolan_group / tools
-
-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.
diff --git a/frag_package/fragmentation.py b/frag_package/fragmentation.py
deleted file mode 100644
index 7dba6091ec1ee1973862c36c94b483729955b4ff..0000000000000000000000000000000000000000
--- a/frag_package/fragmentation.py
+++ /dev/null
@@ -1,36 +0,0 @@
-import random
-
-
-dna_seq = {
- "ATAACATGTGGATGGCCAGTGGTCGGTTGTTACACGCCTACCGCGATGCTGAATGACCCGGACTAGAGTGGCGAAATTTATGGCGTGTGACCCGTTATGC": 100,
- "TCCATTTCGGTCAGTGGGTCATTGCTAGTAGTCGATTGCATTGCCATTCTCCGAGTGATTTAGCGTGACAGCCGCAGGGAACCCATAAAATGCAATCGTA": 100
-}
-
-mean_length = 12
-std = 1
-
-term_frags = []
-for seq, counts in dna_seq.items():
- for _ in range(counts):
- n_cuts = int(len(seq)/mean_length)
- cuts = random.sample(range(1,len(seq)-1), n_cuts)
- cuts.sort()
- cuts.insert(0,0)
- term_frag = ""
- for i, val in enumerate(cuts):
- if i == len(cuts)-1:
- fragment = seq[val:cuts[-1]]
- else:
- fragment = seq[val:cuts[i+1]]
- if mean_length-std <= len(fragment) <= mean_length+std:
- term_frag = fragment
- if term_frag == "":
- continue
- else:
- term_frags.append(term_frag)
-
-with open('terminal_frags.txt', 'w') as f:
- for line in term_frags:
- f.write(line)
- f.write('\n')
-
diff --git a/frag_package/fragmentation_v2.py b/frag_package/fragmentation_v2.py
deleted file mode 100644
index bce9ca91cc627b90cdd85e53fb00519d7c3460a0..0000000000000000000000000000000000000000
--- a/frag_package/fragmentation_v2.py
+++ /dev/null
@@ -1,63 +0,0 @@
-import re
-
-import numpy as np
-import pandas as pd
-
-
-def fasta_process(fasta_file):
- with open(fasta_file, "r") as f:
- lines = f.readlines()
-
- ident_pattern = re.compile('>(\S+)')
- seq_pattern = re.compile('^(\S+)$')
-
- genes = {}
- for line in lines:
- if ident_pattern.search(line):
- seq_id = (ident_pattern.search(line)).group(1)
- elif seq_id in genes.keys():
- genes[seq_id] += (seq_pattern.search(line)).group(1)
- else:
- genes[seq_id] = (seq_pattern.search(line)).group(1)
- return genes
-
-def fragmentation(fasta_file, counts_file, mean_length, std):
- fasta = fasta_process(fasta_file)
- seq_counts = pd.read_csv(counts_file, names = ["seqID", "count"])
-
- nucs = ['A','T','G','C']
- mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
-
- term_frags = []
- for seq_id, seq in fasta.items():
- counts = seq_counts[seq_counts["seqID"] == seq_id]["count"]
- for _ in range(counts):
- n_cuts = int(len(seq)/mean_length)
-
- # non-uniformly random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
- # assume fragmentation by sonication for NGS workflow
- cuts = []
- cut_nucs = np.random.choice(nucs, n_cuts, p=mononuc_freqs)
- for nuc in cut_nucs:
- nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
- pos = np.random.choice(nuc_pos)
- while pos in cuts:
- pos = np.random.choice(nuc_pos)
- cuts.append(pos)
-
- cuts.sort()
- cuts.insert(0,0)
- term_frag = ""
- for i, val in enumerate(cuts):
- if i == len(cuts)-1:
- fragment = seq[val+1:cuts[-1]]
- else:
- fragment = seq[val:cuts[i+1]]
- if mean_length-std <= len(fragment) <= mean_length+std:
- term_frag = fragment
- if term_frag == "":
- continue
- else:
- term_frags.append(term_frag)
- return term_frags
-
diff --git a/frag_package/main.py b/frag_package/main.py
deleted file mode 100644
index 661c8f370c844f633823dc44ba22f6cb0a57c6a1..0000000000000000000000000000000000000000
--- a/frag_package/main.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import argparse
-
-from fragmentation_v2 import fragmentation
-from utils import check_positive, extant_file
-
-
-def main(args):
- fasta, seq_counts, mean_length, std = args
-
- term_frags = fragmentation(fasta, seq_counts, mean_length, std)
- with open('terminal_frags.txt', 'w') as f:
- for line in term_frags:
- f.write(line)
- f.write('\n')
-
-# Parse command-line arguments
-def parse_arguments():
- parser = argparse.ArgumentParser(description="Takes as input FASTA file of cDNA sequences, a CSV with sequence counts, and mean and std. dev. of fragment lengths. Outputs most terminal fragment (within desired length range) for each sequence.")
-
- parser.add_argument('--fasta', required=True, type=extant_file, help="FASTA file with cDNA sequences")
- parser.add_argument('--counts', required=True, type=extant_file, help="CSV file with sequence counts")
- parser.add_argument('--mean', required = False, default = 10, type = check_positive, help="Mean fragment length (default: 10)")
- parser.add_argument('--std', required = False, default = 1, type = check_positive, help="Standard deviation fragment length (defafult: 1)")
- args = parser.parse_args()
-
- return args.fasta, args.counts, args.mean, args.std
-
-
-if __name__ == '__main__':
- arguments = parse_arguments()
- main(arguments)
\ No newline at end of file
diff --git a/frag_package/utils.py b/frag_package/utils.py
deleted file mode 100644
index 2212bbc61d3db2fd0c55f8d85f52866fb31c2d07..0000000000000000000000000000000000000000
--- a/frag_package/utils.py
+++ /dev/null
@@ -1,24 +0,0 @@
-import argparse
-import os.path
-
-
-# found on https://stackoverflow.com/questions/11540854/file-as-command-line-argument-for-argparse-error-message-if-argument-is-not-va
-def extant_file(x):
- """
- 'Type' for argparse - checks that file exists but does not open.
- """
- if not os.path.exists(x):
- # Argparse uses the ArgumentTypeError to give a rejection message like:
- # error: argument input: x does not exist
- raise argparse.ArgumentTypeError("{0} does not exist".format(x))
- elif not x.endswith((".fasta", ".fa", ".csv")):
- raise argparse.ArgumentTypeError("{0} is not the correct file format".format(x))
- return x
-
-# found on https://stackoverflow.com/questions/14117415/in-python-using-argparse-allow-only-positive-integers
-def check_positive(value):
- ivalue = int(value)
- if ivalue <= 0:
- raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
- return ivalue
-
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