From 995f7d7bc0aad52eb551df3e7ffe5caf9daa6953 Mon Sep 17 00:00:00 2001
From: "hugo.madgeleon" <hugo.madgeleon@stud.unibas.ch>
Date: Thu, 8 Dec 2022 18:34:29 +0100
Subject: [PATCH] linting + small fixes
---
.gitignore | 1 +
terminal-fragment-selector/fragmentation.py | 56 ++++++++++++----
terminal-fragment-selector/main.py | 71 +++++++++++++++------
terminal-fragment-selector/utils.py | 57 +++++++++++++----
4 files changed, 141 insertions(+), 44 deletions(-)
diff --git a/.gitignore b/.gitignore
index fa5a841..510b9ee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -52,6 +52,7 @@ Temporary Items
# Ignore all local history of files
.history
.ionide
+.vscode
# End of https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode
diff --git a/terminal-fragment-selector/fragmentation.py b/terminal-fragment-selector/fragmentation.py
index 6a1e68a..ff7c73f 100644
--- a/terminal-fragment-selector/fragmentation.py
+++ b/terminal-fragment-selector/fragmentation.py
@@ -1,3 +1,4 @@
+"""Fragment sequences."""
import re
import numpy as np
@@ -5,9 +6,19 @@ import pandas as pd
def fasta_process(fasta_file):
+ """
+ Pre-process FASTA file.
+
+ Args:
+ fasta_file (fasta): FASTA file with cDNA sequences
+
+ Returns:
+ dict: Dictionary of gene sequence IDs and their sequence
+ """
with open(fasta_file, "r") as f:
lines = f.readlines()
+ # Tanya, try \\S instead of \S and see if that works
ident_pattern = re.compile('>(\S+)')
seq_pattern = re.compile('^(\S+)$')
@@ -21,24 +32,44 @@ def fasta_process(fasta_file):
genes[seq_id] = (seq_pattern.search(line)).group(1)
return genes
-def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_prob, c_prob):
+
+def fragmentation(fasta_file, counts_file, mean_length, std,
+ a_prob, t_prob, g_prob, c_prob):
+ """
+ Fragment cDNA sequences and select terminal fragment.
+
+ Args:
+ fasta_file (fasta): FASTA file with cDNA sequences
+ counts_file (text): CSV or TSV file woth sequence counts
+ mean_length (int): mean length of desired fragments
+ std (int): standard deviation of desired fragment lengths
+ a_prob (float): probability of nucleotide A
+ t_prob (float): probability of nucleotide T
+ g_prob (float): probability of nucleotide G
+ c_prob (float): probability of nucleotide C
+
+ Returns:
+ list: list of selected terminal fragments
+ """
fasta = fasta_process(fasta_file)
- seq_counts = pd.read_csv(counts_file, names = ["seqID", "count"])
+ seq_counts = pd.read_csv(counts_file,
+ names=["seqID", "count"])
- # nucs = ['A','T','G','C']
- # mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
- nuc_probs = {'A':a_prob, 'T':t_prob, 'G':g_prob, 'C':c_prob} # calculated using https://www.nature.com/articles/srep04532#MOESM1
+ # calculated using https://www.nature.com/articles/srep04532#MOESM1
+ nuc_probs = {'A': a_prob, 'T': t_prob, 'G': g_prob, 'C': c_prob}
- term_frags = []
+ term_frags = []
for seq_id, seq in fasta.items():
counts = seq_counts[seq_counts["seqID"] == seq_id]["count"]
- for _ in range(counts):
+ for _ in range(counts):
n_cuts = int(len(seq)/mean_length)
-
- # non-uniformly random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
+
+ # non-uniformly random DNA fragmentation implementation based on
+ # https://www.nature.com/articles/srep04532#Sec1
# assume fragmentation by sonication for NGS workflow
cuts = []
- cut_nucs = np.random.choice(list(nuc_probs.keys()), n_cuts, p=list(nuc_probs.values()))
+ cut_nucs = np.random.choice(list(nuc_probs.keys()),
+ n_cuts, p=list(nuc_probs.values()))
for nuc in cut_nucs:
nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
pos = np.random.choice(nuc_pos)
@@ -46,8 +77,8 @@ def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_p
pos = np.random.choice(nuc_pos)
cuts.append(pos)
- cuts.sort()
- cuts.insert(0,0)
+ cuts.sort()
+ cuts.insert(0, 0)
term_frag = ""
for i, val in enumerate(cuts):
if i == len(cuts)-1:
@@ -61,4 +92,3 @@ def fragmentation(fasta_file, counts_file, mean_length, std, a_prob, t_prob, g_p
else:
term_frags.append(term_frag)
return term_frags
-
diff --git a/terminal-fragment-selector/main.py b/terminal-fragment-selector/main.py
index 0088de4..b91fb2f 100644
--- a/terminal-fragment-selector/main.py
+++ b/terminal-fragment-selector/main.py
@@ -1,35 +1,70 @@
+"""Receive command line arguments, fragment, and output fragments."""
import argparse
-from fragmentation_v2 import fragmentation
+from fragmentation import fragmentation
from utils import check_positive, extant_file, check_prob
-def main(args):
+def main(args):
+ """
+ Use CLI arguments to fragment sequences and output text file \
+ with selected terminal fragments.
+
+ Args:
+ args (parser): list of arguments from CLI.
+ """
fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob = args
- term_frags = fragmentation(fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob)
+ term_frags = fragmentation(fasta, seq_counts, mean_length, std,
+ a_prob, t_prob, g_prob, c_prob)
with open('terminal_frags.txt', 'w') as f:
for line in term_frags:
- f.write(line)
- f.write('\n')
+ f.write(f"{line}\n")
+
-# Parse command-line arguments
def parse_arguments():
- parser = argparse.ArgumentParser(description="Takes as input FASTA file of cDNA sequences, a CSV with sequence counts, and mean and std. dev. of fragment lengths and 4 nucleotide probabilities for the cuts. Outputs most terminal fragment (within desired length range) for each sequence.")
-
- parser.add_argument('--fasta', required=True, type=extant_file, help="FASTA file with cDNA sequences")
- parser.add_argument('--counts', required=True, type=extant_file, help="CSV file with sequence counts")
- parser.add_argument('--mean', required = False, default = 300, type = check_positive, help="Mean fragment length (default: 10)")
- parser.add_argument('--std', required = False, default = 60, type = check_positive, help="Standard deviation fragment length (defafult: 1)")
- parser.add_argument('--A_prob', required=False, default = 0.22, type=check_prob, help="Probability cut happens after nucleotide A")
- parser.add_argument('--T_prob', required=False, default = 0.25, type=check_prob, help="Probability cut happens after nucleotide T")
- parser.add_argument('--G_prob', required=False, default = 0.25, type=check_prob, help="Probability cut happens after nucleotide G")
- parser.add_argument('--C_prob', required=False, default = 0.28, type=check_prob, help="Probability cut happens after nucleotide C")
+ """
+ Request parameters from user on CLI.
+
+ Returns:
+ parser: list of arguments from CLI.
+ """
+ parser = argparse.ArgumentParser(description="""Takes as input FASTA file
+ of cDNA sequences, a CSV with sequence
+ counts, and mean and std. dev. of fragment
+ lengths and 4 nucleotide probabilities
+ for the cuts. Outputs most terminal
+ fragment (within desired length range)
+ for each sequence.""")
+
+ parser.add_argument('--fasta', required=True, type=extant_file,
+ help="FASTA file with cDNA sequences")
+ parser.add_argument('--counts', required=True, type=extant_file,
+ help="CSV file with sequence counts")
+ parser.add_argument('--mean', required=False, default=300,
+ type=check_positive,
+ help="Mean fragment length (default: 10)")
+ parser.add_argument('--std', required=False, default=60,
+ type=check_positive,
+ help="Standard deviation fragment length \
+ (defafult: 1)")
+ parser.add_argument('--A_prob', required=False, default=0.22,
+ type=check_prob,
+ help="Probability cut happens after nucleotide A")
+ parser.add_argument('--T_prob', required=False, default=0.25,
+ type=check_prob,
+ help="Probability cut happens after nucleotide T")
+ parser.add_argument('--G_prob', required=False, default=0.25,
+ type=check_prob,
+ help="Probability cut happens after nucleotide G")
+ parser.add_argument('--C_prob', required=False, default=0.28,
+ type=check_prob,
+ help="Probability cut happens after nucleotide C")
args = parser.parse_args()
-
+
return args
if __name__ == '__main__':
arguments = parse_arguments()
- main(arguments)
\ No newline at end of file
+ main(arguments)
diff --git a/terminal-fragment-selector/utils.py b/terminal-fragment-selector/utils.py
index aced683..0e421ca 100644
--- a/terminal-fragment-selector/utils.py
+++ b/terminal-fragment-selector/utils.py
@@ -1,29 +1,60 @@
+"""Utility functions for command line arguments."""
import argparse
import os.path
-# found on https://stackoverflow.com/questions/11540854/file-as-command-line-argument-for-argparse-error-message-if-argument-is-not-va
+# found on shorturl.at/vzAX4
def extant_file(x):
- """
- 'Type' for argparse - checks that file exists but does not open.
- """
if not os.path.exists(x):
# Argparse uses the ArgumentTypeError to give a rejection message like:
# error: argument input: x does not exist
raise argparse.ArgumentTypeError("{0} does not exist".format(x))
elif not x.endswith((".fasta", ".fa", ".csv")):
- raise argparse.ArgumentTypeError("{0} is not the correct file format".format(x))
+ raise argparse.ArgumentTypeError("""{0} is not the correct
+ file format""".format(x))
return x
-# found on https://stackoverflow.com/questions/14117415/in-python-using-argparse-allow-only-positive-integers
+
def check_positive(value):
- ivalue = int(value)
- if ivalue <= 0:
- raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
- return ivalue
+ """Check input value is a positive integer.
+
+ Args:
+ value (string): command line parameter
+
+ Raises:
+ argparse.ArgumentTypeError: received a negative integer
+ argparse.ArgumentTypeError: received a non-integer value
+
+ Returns:
+ integer: integer version of input value
+ """
+ try:
+ ivalue = round(float(value))
+ if ivalue <= 0:
+ raise argparse.ArgumentTypeError(f"""Expected positive integer,
+ got negative integer: {value}""")
+ except ValueError as exc:
+ raise argparse.ArgumentTypeError(f"""Expected positive integer,
+ got: {value}""") from exc
+ else:
+ return ivalue
+
def check_prob(value):
+ """
+ Check probability value is within ]0,1] range.
+
+ Args:
+ value (string): command line parameter
+
+ Raises:
+ argparse.ArgumentTypeError: received a value outside valid range
+
+ Returns:
+ float: float version of input value
+ """
pvalue = float(value)
- if pvalue <= 0 or pvalue>1:
- raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
- return pvalue
\ No newline at end of file
+ if pvalue <= 0 or pvalue > 1:
+ raise argparse.ArgumentTypeError("""%s is an invalid positive int
+ value""" % value)
+ return pvalue
--
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