From d3f38575386518350c31b64b7752e9686f0c964d Mon Sep 17 00:00:00 2001
From: Hugo Madge Leon <hugo.madgeleon@stud.unibas.ch>
Date: Fri, 9 Dec 2022 15:20:47 +0000
Subject: [PATCH] Fix all issues from review except frag theory
---
terminal-fragment-selector/fragmentation.py | 42 ++------
terminal-fragment-selector/main.py | 112 ++++++++++++++++----
terminal-fragment-selector/utils.py | 23 +---
3 files changed, 103 insertions(+), 74 deletions(-)
diff --git a/terminal-fragment-selector/fragmentation.py b/terminal-fragment-selector/fragmentation.py
index ff7c73f..f85b1e8 100644
--- a/terminal-fragment-selector/fragmentation.py
+++ b/terminal-fragment-selector/fragmentation.py
@@ -5,42 +5,16 @@ import numpy as np
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+)$')
-
- genes = {}
- for line in lines:
- if ident_pattern.search(line):
- seq_id = (ident_pattern.search(line)).group(1)
- elif seq_id in genes.keys():
- genes[seq_id] += (seq_pattern.search(line)).group(1)
- else:
- 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: dict, seq_counts: pd.DataFrame,
+ mean_length: int, std: int,
+ a_prob: float, t_prob: float, g_prob: float, c_prob: float
+ ) -> list:
"""
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
+ fasta_file (dict): dictionary of {transcript IDs: sequences}
+ counts_file (pd.DataFrame): dataframe with sequence counts and IDs
mean_length (int): mean length of desired fragments
std (int): standard deviation of desired fragment lengths
a_prob (float): probability of nucleotide A
@@ -51,10 +25,6 @@ def fragmentation(fasta_file, counts_file, mean_length, std,
Returns:
list: list of selected terminal fragments
"""
- fasta = fasta_process(fasta_file)
- seq_counts = pd.read_csv(counts_file,
- names=["seqID", "count"])
-
# calculated using https://www.nature.com/articles/srep04532#MOESM1
nuc_probs = {'A': a_prob, 'T': t_prob, 'G': g_prob, 'C': c_prob}
diff --git a/terminal-fragment-selector/main.py b/terminal-fragment-selector/main.py
index b91fb2f..73368a1 100644
--- a/terminal-fragment-selector/main.py
+++ b/terminal-fragment-selector/main.py
@@ -1,11 +1,16 @@
-"""Receive command line arguments, fragment, and output fragments."""
+"""Receive command line arguments, fragment sequences, and output fragments."""
import argparse
+import logging
+from Bio import SeqIO
+import numpy as np
+import pandas as pd
+from pathlib import Path
from fragmentation import fragmentation
-from utils import check_positive, extant_file, check_prob
+from utils import check_positive, check_prob
-def main(args):
+def main(args: argparse.Namespace):
"""
Use CLI arguments to fragment sequences and output text file \
with selected terminal fragments.
@@ -13,34 +18,88 @@ def main(args):
Args:
args (parser): list of arguments from CLI.
"""
- fasta, seq_counts, mean_length, std, a_prob, t_prob, g_prob, c_prob = args
+ fasta_file, counts_file, output, mean_length, std = args[0:5]
+ a_prob, t_prob, g_prob, c_prob, chunk_size, sep = args[5:]
- 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(f"{line}\n")
+ # Create or wipe output file
+ open(output, "w").close()
+ logger.info("Checking validity of files...")
+ fasta, seq_counts = file_validation(fasta_file, counts_file, sep)
-def parse_arguments():
+ logger.info(f"Fragmentation of {fasta_file}...")
+ fasta_parse = {}
+ for record in fasta:
+ fasta_parse[record.id] = record.seq
+ splits = np.arange(0, len(list(fasta_parse))+chunk_size, chunk_size)
+
+ for i, split in enumerate(splits):
+ fasta_dict = fasta_parse[split:splits[i+1]]
+ term_frags = fragmentation(fasta_dict, seq_counts,
+ mean_length, std,
+ a_prob, t_prob, g_prob, c_prob)
+
+ logger.info(f"Writing batch {i} sequences to {output}...")
+ with open(output, 'a') as f:
+ for line in term_frags:
+ f.write(f"{line}\n")
+
+
+def file_validation(fasta_file: str,
+ counts_file: str,
+ sep: str) -> tuple[dict, pd.DataFrame]:
+ """
+ Validate input files exist and are the correct format.
+
+ Args:
+ fasta_file (str): Input FASTA file path
+ counts_file (str): CSV or TSV counts file path
+ sep (str): Separator for counts file.
+
+ Returns:
+ tuple: fasta and sequence counts variables
+ """
+ with open(fasta_file, "r") as handle:
+ fasta = SeqIO.parse(handle, "fasta")
+ try:
+ any(fasta)
+ except Exception:
+ logger.exception("Input FASTA file is either empty or \
+ incorrect file type.")
+
+ count_path = Path(counts_file)
+ if not count_path.is_file():
+ logger.exception("Input counts file does not exist or isn't a file.")
+ else:
+ if sep == ",":
+ seq_counts = pd.read_csv(counts_file, names=["seqID", "count"])
+ else:
+ seq_counts = pd.read_table(counts_file, names=["seqID", "count"])
+
+ return fasta, seq_counts
+
+
+def parse_arguments() -> argparse.Namespace:
"""
Request parameters from user on CLI.
Returns:
- parser: list of arguments from CLI.
+ argparse.Namespace: object of arguments from CLI.
"""
parser = argparse.ArgumentParser(description="""Takes as input FASTA file
- of cDNA sequences, a CSV with sequence
+ of cDNA sequences, a CSV/TSV 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('--fasta', required=True,
+ help="Path to FASTA file with cDNA sequences")
+ parser.add_argument('--counts', required=True,
+ help="Path to CSV/TSV file with sequence counts")
+ parser.add_argument('-o', '--output', required=True,
+ help="output file path")
parser.add_argument('--mean', required=False, default=300,
type=check_positive,
help="Mean fragment length (default: 10)")
@@ -48,23 +107,36 @@ def parse_arguments():
type=check_positive,
help="Standard deviation fragment length \
(defafult: 1)")
- parser.add_argument('--A_prob', required=False, default=0.22,
+ 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_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_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_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,
+ type=check_positive,
+ help="Chunk size for batch processing")
+ parser.add_argument('--sep', required=False, default=",",
+ type=check_positive,
+ help="Sequence counts file separator.")
args = parser.parse_args()
return args
if __name__ == '__main__':
+ logging.basicConfig(
+ format='[%(asctime)s: %(levelname)s] %(message)s \
+ (module "%(module)s")',
+ level=logging.INFO,
+ )
+ logger = logging.getLogger(__name__)
+
arguments = parse_arguments()
main(arguments)
diff --git a/terminal-fragment-selector/utils.py b/terminal-fragment-selector/utils.py
index 0e421ca..a947411 100644
--- a/terminal-fragment-selector/utils.py
+++ b/terminal-fragment-selector/utils.py
@@ -1,25 +1,12 @@
-"""Utility functions for command line arguments."""
+"""Utility functions for CLI arguments."""
import argparse
-import os.path
-# found on shorturl.at/vzAX4
-def extant_file(x):
- 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))
- return x
-
-
-def check_positive(value):
+def check_positive(value: str) -> int:
"""Check input value is a positive integer.
Args:
- value (string): command line parameter
+ value (str): command line parameter
Raises:
argparse.ArgumentTypeError: received a negative integer
@@ -40,12 +27,12 @@ def check_positive(value):
return ivalue
-def check_prob(value):
+def check_prob(value: str) -> float:
"""
Check probability value is within ]0,1] range.
Args:
- value (string): command line parameter
+ value (str): command line parameter
Raises:
argparse.ArgumentTypeError: received a value outside valid range
--
GitLab