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Commit 11896ade authored by Kathleen Moriarty's avatar Kathleen Moriarty
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fix docstring text

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""" Read Sequencing
"""Read Sequencing!
Simulate the sequencing of reads on the template of terminal fragments and simulates reads of these fragments.
Author: Kathleen Moriarty
Class: Programming for Life Sciences
"""
def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_seq_cyc):
"""Reads a fasta-formatted file of terminal fragments and simulates reads of these fragments.
def read_sequencing(
frag_file_name,
output_file_name,
num_reads,
read_len,
num_seq_cyc,
) -> 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
......@@ -13,19 +20,17 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
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.
:param output_file_name: file name where to store the output
:param num_seq_cyc: integer of number of cycles
:param read_len: integer of identical read length
:param num_reads: number of total reads to simulate
:param frag_file_name: input file of terminal fragments
Output:
Fasta-formatted file ("../output/reads.csv") of reads of identical length, representing 5’
ends of the terminal fragments
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 (string): input file of terminal fragments
output_file_name (string): file name where to store the output
num_reads: number of total reads to simulate
read_len: integer of identical read length
num_seq_cyc: integer of number of cycles
"""
# Import classes
from random import choices, randrange
import numpy as np
......
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