From 551c2056c7cff2a2ebd4404d0cf5faff2bfbedff Mon Sep 17 00:00:00 2001
From: "hugo.madgeleon" <hugo.madgeleon@stud.unibas.ch>
Date: Sun, 11 Dec 2022 19:52:22 +0100
Subject: [PATCH] tanya's changes
---
term_frag_sel/cli.py | 16 +++++------
term_frag_sel/fragmentation.py | 50 ++++++++++++++++++++++++++++------
tests/test_frag.py | 44 ++++++++++++++++++++++++++----
tests/test_utils.py | 6 ----
4 files changed, 89 insertions(+), 27 deletions(-)
diff --git a/term_frag_sel/cli.py b/term_frag_sel/cli.py
index a9b8e95..2495d85 100644
--- a/term_frag_sel/cli.py
+++ b/term_frag_sel/cli.py
@@ -35,8 +35,8 @@ def main(args: argparse.Namespace):
fasta_dict = fasta_parse[split:splits[i+1]]
term_frags = fragmentation(fasta_dict, seq_counts,
args.mean, args.std,
- args.A_prob, args.T_prob,
- args.G_prob, args.C_prob)
+ args.a_prob, args.t_prob,
+ args.g_prob, args.c_prob)
logger.info("Writing batch %s sequences to %s...", i, args.output)
with open(args.output, 'a', encoding="utf-8") as out_file:
@@ -97,21 +97,21 @@ def parse_arguments() -> argparse.Namespace:
help="output file path")
parser.add_argument('--mean', required=False, default=300,
type=check_positive,
- help="Mean fragment length (default: 10)")
+ help="Mean fragment length (default: 300)")
parser.add_argument('--std', required=False, default=60,
type=check_positive,
help="Standard deviation fragment length \
- (defafult: 1)")
- parser.add_argument('-a', '--A_prob', required=False, default=0.22,
+ (defafult: 60)")
+ parser.add_argument('-a', '--a_prob', required=False, default=0.22,
type=check_prob,
help="Probability cut happens after nucleotide A")
- parser.add_argument('-t', '--T_prob', required=False, default=0.25,
+ parser.add_argument('-t', '--t_prob', required=False, default=0.25,
type=check_prob,
help="Probability cut happens after nucleotide T")
- parser.add_argument('-g', '--G_prob', required=False, default=0.25,
+ parser.add_argument('-g', '--g_prob', required=False, default=0.25,
type=check_prob,
help="Probability cut happens after nucleotide G")
- parser.add_argument('-c', '--C_prob', required=False, default=0.28,
+ parser.add_argument('-c', '--c_prob', required=False, default=0.28,
type=check_prob,
help="Probability cut happens after nucleotide C")
parser.add_argument('-s', '--size', required=False, default=10000,
diff --git a/term_frag_sel/fragmentation.py b/term_frag_sel/fragmentation.py
index 302fe6f..7444ff8 100644
--- a/term_frag_sel/fragmentation.py
+++ b/term_frag_sel/fragmentation.py
@@ -4,6 +4,38 @@ import re
import numpy as np
import pandas as pd # type: ignore
+def get_cut_number(seq_len: int, mean: float) -> int:
+ """Get the number of cuts for a particular sequence.
+
+ Args:
+ seq_len (int): length of sequence/number of nucleotides in the sequence
+ mean (float): mean fragment length
+
+ Returns:
+ int: number of cuts
+ """
+ cuts_distribution = [] # distribution of cut numbers (n_cuts)
+
+ # 1000 iterations should not be too computationally inefficient given the nature of the code
+ for _ in range(1000):
+ n_cuts = 0
+ len_sum = 0
+ while True:
+ len_sum += np.random.exponential(scale = mean)
+ if len_sum < seq_len:
+ n_cuts += 1
+ else:
+ cuts_distribution.append(n_cuts)
+ break
+
+ cuts_distribution.sort()
+ cut_counts = {x:cuts_distribution.count(x) for x in cuts_distribution}
+ cut_probs = [x/1000 for x in cut_counts.values()]
+
+ # randomly ick no. of cut from cut distribution based on probability of cut numbers
+ n_cuts = np.random.choice(list(cut_counts.keys()), p = cut_probs)
+
+ return n_cuts
def fragmentation(fasta: dict, seq_counts: pd.DataFrame,
mean_length: int = 100, std: int = 10,
@@ -32,7 +64,10 @@ def fragmentation(fasta: dict, seq_counts: pd.DataFrame,
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)
+ seq_len = len(seq)
+
+ # pick no. of cuts from gauss fragment length distribution
+ n_cuts = get_cut_number(seq_len, mean_length)
# non-uniformly random DNA fragmentation implementation based on
# https://www.nature.com/articles/srep04532#Sec1
@@ -50,13 +85,12 @@ def fragmentation(fasta: dict, seq_counts: pd.DataFrame,
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
+
+ # check if 3' fragment is in the correct size range
+ fragment = seq[cuts[-1]:len(seq)]
+ if mean_length-std <= len(fragment) <= mean_length+std:
+ term_frag = fragment
+
if term_frag != "":
term_frags.append(term_frag)
diff --git a/tests/test_frag.py b/tests/test_frag.py
index d97b176..a90eaf6 100644
--- a/tests/test_frag.py
+++ b/tests/test_frag.py
@@ -1,13 +1,17 @@
"""Test utils.py functions."""
+import random
import pytest
from Bio import SeqIO
-from term_frag_sel.fragmentation import fragmentation # type: ignore
+from term_frag_sel.fragmentation import fragmentation, get_cut_number # type: ignore
with open("tests/test_files/test.fasta", "r", encoding="utf-8") as handle:
fasta = SeqIO.parse(handle, "fasta")
-# have to create the counts file
+seq_counts = {}
+for entry in fasta:
+ name, sequence = entry.id, str(entry.seq)
+ seq_counts[name] = random.randint(50,150)
MU = 100
STD = 10
@@ -16,8 +20,38 @@ C_PROB = 0.28
T_PROB = 0.25
G_PROB = 0.25
+def test_get_cut_number():
+ """Test get_cut_number function."""
+ assert get_cut_number(100,20,4) <= 15 and get_cut_number(100,20,4) >= 0
-def test_frag():
- """Test fragmentation function."""
+ with pytest.raises(ValueError):
+ get_cut_number(seq_len = 'a', mean = 4, std = 2.3) # error if seq_len not int
+ with pytest.raises(ValueError):
+ get_cut_number(seq_len = 10, mean = 'a', std = 2.3) # error if mean not int
+ with pytest.raises(ValueError):
+ get_cut_number(seq_len = 10, mean = 3, std = 'a') # error if std not float
with pytest.raises(TypeError):
- fragmentation()
+ get_cut_number(seq_len = 10, mean = 3) # error if there is a missing argument
+
+def test_fragmentation():
+ """Test fragmentation function."""
+ assert isinstance(fragmentation(fasta, seq_counts), list)
+
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 'a', std = 10,
+ a_prob = 0.22, t_prob = 0.25,g_prob = 0.25, c_prob = 0.28)
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 100, std = 'a',
+ a_prob = 0.22, t_prob = 0.25,g_prob = 0.25, c_prob = 0.28)
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 100, std = 10,
+ a_prob = 'a', t_prob = 0.25,g_prob = 0.25, c_prob = 0.28)
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 100, std = 10,
+ a_prob = 0.22, t_prob = 'a',g_prob = 0.25, c_prob = 0.28)
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 100, std = 10,
+ a_prob = 0.22, t_prob = 0.25,g_prob = 'a', c_prob = 0.28)
+ with pytest.raises(ValueError):
+ fragmentation(fasta, seq_counts, mean_length = 100, std = 10,
+ a_prob = 0.22, t_prob = 0.25,g_prob = 0.25, c_prob = 'a')
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 36084a6..c7d7be2 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,9 +1,4 @@
"""Test utils.py functions."""
-<<<<<<< HEAD
-import pytest
-
-from
-=======
import argparse
import pytest
@@ -40,4 +35,3 @@ def test_prob():
check_prob("string")
with pytest.raises(ValueError):
check_prob("")
->>>>>>> hugo_new
--
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