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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 Author: Kathleen Moriarty
Class: Programming for Life Sciences
""" """
def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_seq_cyc): def read_sequencing(
"""Reads a fasta-formatted file of terminal fragments and simulates reads of these fragments. 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 Simulate the sequencing of reads on the template of terminal
fragments. Reads are copies of fixed length starting 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 ...@@ -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 is larger than the fragment length, sequencing would in
principle proceed into the 3' adaptor and then would perhaps principle proceed into the 3' adaptor and then would perhaps
yield random bases. For simplicity, here we assume that random yield random bases. For simplicity, here we assume that random
nucleotides are introduced in this case. nucleotides are introduced in this case. Saves a fasta-formatted
file of reads of identical length, representing 5’
:param output_file_name: file name where to store the output ends of the terminal fragments as .txt.
:param num_seq_cyc: integer of number of cycles
:param read_len: integer of identical read length Args:
:param num_reads: number of total reads to simulate frag_file_name (string): input file of terminal fragments
:param frag_file_name: input file of terminal fragments output_file_name (string): file name where to store the output
num_reads: number of total reads to simulate
Output: read_len: integer of identical read length
Fasta-formatted file ("../output/reads.csv") of reads of identical length, representing 5’ num_seq_cyc: integer of number of cycles
ends of the terminal fragments
""" """
# Import classes # Import classes
from random import choices, randrange from random import choices, randrange
import numpy as np import numpy as np
......
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