From 204584b0b48e63fc92e3f48a000a8e98e1b90cb7 Mon Sep 17 00:00:00 2001
From: clara <clara@dyn-39-19.mobile.unibas.ch>
Date: Fri, 11 Nov 2022 15:52:38 +0100
Subject: [PATCH] modified: read_sequencer_package/modules.py
---
read_sequencer_package/modules.py | 64 ++++++++++++++++++++++++++-----
1 file changed, 54 insertions(+), 10 deletions(-)
diff --git a/read_sequencer_package/modules.py b/read_sequencer_package/modules.py
index ca84a64..a65561a 100644
--- a/read_sequencer_package/modules.py
+++ b/read_sequencer_package/modules.py
@@ -1,11 +1,13 @@
def read_in_fasta(file_path):
'''
- This function reads in FASTA files
+ This function reads in FASTA files.
- argument is file_path
+ Args:
+ file_path (str): A file path directing to the fasta file.
- it returns a dictionary with the sequences
+ Returns:
+ Dict: It returns a dictionary with sequences.
'''
sequences = {}
@@ -21,13 +23,17 @@ def read_in_fasta(file_path):
f.close()
return sequences
-def read_sequence(seq, read_length, padding_probabilities=None):
+def read_sequence(seq, read_length):
'''
- This function reads sequences
- arguments: seq is a list of sequences
- padding_probabilities is a number??
+ This function reads a sequence of a specific read length and adds additional nucleotides if the sequence is
+ smaller then the requested length or cuts the sequence if its longer.
- returns sequenced element
+ Args:
+ seq (str): the sequence to read
+ read_length (int): length of reads
+
+ Returns:
+ str: returns sequenced element
'''
from random import choice
@@ -45,16 +51,54 @@ def read_sequence(seq, read_length, padding_probabilities=None):
return sequenced
def simulate_sequencing(sequences, read_length):
+ """
+ Simulates sequencing.
+
+ Args:
+ sequences (dict): Dictionary of sequences to sequence.
+ read_length (int): length of reads
+
+ Returns:
+ dict: of n sequences as values
+ """
results = {}
for index, key in enumerate(sequences):
results[key] = read_sequence(sequences[key],read_length=read_length)
return results
+import random
+def generate_sequences(n, mean, sd):
+ """
+ Generates random sequences.
+
+ Args:
+ n (int): Amount of sequences to generate.
+ mean (int): mean length of sequence (gaussian distribution).
+ sd (float): standart deviation of length of sequence (gaussian distribution).
+
+ Returns:
+ dict: of n sequences
+ """
+ dict1 = {}
+ for i in range(n):
+ keys = range(n)
+ seq = ""
+ nt = ["A", "T", "C", "G"]
+ for value in range(round(random.gauss(mean, sd))):
+ seq = seq + random.choice(nt)
+ dict1[keys[i]] = seq
+ return dict1
+
def write_fasta(sequences, file_path):
"""
- Takes a dictionary and writes it to a fasta file
- Must specify the filename when caling the function
+ Takes a dictionary and writes it to a fasta file.
+ Must specify the filename when calling the function.
+
+ Args:
+ sequences (dict): Dictionary of sequence.
+ file_path (str): A file path directing to the output folder.
+
"""
from textwrap import wrap
with open(file_path, "w") as outfile:
--
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