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\ No newline at end of file

LICENSE

-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.

frag_package/fragmentation.py

-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')
-

frag_package/fragmentation_v2.py

-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
-

frag_package/main.py

-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

frag_package/utils.py

-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
-