From 59e66531d2c7e6d9a5b7cf77db4c0a20ea218208 Mon Sep 17 00:00:00 2001
From: "kathleen.moriarty" <kathleen.moriarty@unibas.ch>
Date: Mon, 3 Jan 2022 14:29:24 +0100
Subject: [PATCH] remove old read_sequencing.py
---
src/read_sequencing.py | 98 ------------------------------------------
1 file changed, 98 deletions(-)
delete mode 100644 src/read_sequencing.py
diff --git a/src/read_sequencing.py b/src/read_sequencing.py
deleted file mode 100644
index dfd7da9..0000000
--- a/src/read_sequencing.py
+++ /dev/null
@@ -1,98 +0,0 @@
-"""Read Sequencing.
-
-Simulate the sequencing of reads on the template of terminal fragments and simulates reads of these fragments.
-Author: Kathleen Moriarty
-"""
-# Imports from built-in modules
-from random import choices
-from typing import List
-from pathlib import Path
-
-
-def read_sequencing(
- frag_file_name: Path,
- output_file_name: Path = Path.cwd() / 'output_reads.txt',
- num_reads: int = 1000,
- read_len: int = 80,
-) -> None:
- """Reads a fasta-formatted file of terminal fragments and simulates reads.
-
- Simulate the sequencing of reads on the template of terminal
- fragments. Reads are copies of fixed length starting
- from the 5' end of fragments. If the desired read length
- is larger than the fragment length, sequencing would in
- principle proceed into the 3' adaptor and then would perhaps
- yield random bases. For simplicity, here we assume that random
- nucleotides are introduced in this case. Saves a fasta-formatted
- file of reads of identical length, representing 5’
- ends of the terminal fragments as .txt.
-
- Args:
- frag_file_name: input file path of terminal fragments
- output_file_name: output file path where to store the output
- num_reads: number of total reads to simulate
- read_len: integer of identical read length
- """
- # Read data from terminal fragment file
- # Store fragment descriptions in a list
- frag_desc = [] # type: List[str]
-
- with open(frag_file_name, 'r') as f:
- frag_line = f.readline()
- # Store all fragments as a list to parse later
- frag_list = [] # type: List[str]
- # Store combined fragment lines
- frag_str = ""
- while frag_line != "":
- # To stop when the end of file is reached
- if frag_line.startswith('>'):
- # Determine if this is the first fragment in the file
- # Ignore the description line (starting with >) of the first fragment
- if not (len(frag_list) == 0 and frag_str == ""):
- # Not the first fragment. Append to list.
- frag_list.append(frag_str)
- frag_str = ""
- # Store description line for output file
- frag_desc.append(frag_line)
- else:
- frag_str = frag_str + frag_line.rstrip("\n")
- # Read next line
- frag_line = f.readline()
- frag_list.append(frag_str)
-
- # Store list of random nucleotides from which to sample when read length is too short
- nucleotides = ['A', 'C', 'G', 'T']
-
- # Calculate sum of all lengths to determine the relative abundance for that fragment
- sum_frags = sum(map(len, frag_list))
-
- # Open the file to save the reads
- with open(output_file_name, 'w') as fw:
-
- # Loop through fasta fragments that start with 5'
- for frag in frag_list:
- # Determine number of reads to create from this fragment
- # This might not always provide an exact number of reads that were asked
- # TODO resolve this issue
- num_frag_reads = round((len(frag)/sum_frags) * num_reads)
-
- for i in range(0, num_frag_reads):
- # If the read length is less than the required length given by the parameter,
- # then add random nucleotides
- if len(frag) < read_len:
-
- # Calculate number of random nucleotides to add to the end of the read
- diff = read_len - len(frag)
-
- # Select random nucleotides from list of possible
- rand_samp = choices(nucleotides, k=diff)
-
- # Add the random list to the read and save
- tmp_read = frag[0:len(frag)] + ''.join(rand_samp)
- else:
- # Save subset of fragment as read
- tmp_read = frag[0:read_len]
-
- # Write read to file and original fragment description
- fw.write(frag_desc[frag_list.index(frag)])
- fw.write(tmp_read + "\n\n")
--
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