From b8924ea1cc74569a9de37fd0c90f7dea374c3eb5 Mon Sep 17 00:00:00 2001
From: Hugo Madge Leon <hugo.madgeleon@stud.unibas.ch>
Date: Fri, 9 Dec 2022 18:47:39 +0000
Subject: [PATCH] Remove build files
---
.gitignore | 3 +-
build/lib/term_frag_sel/__init__.py | 1 -
build/lib/term_frag_sel/cli.py | 137 -----------------------
build/lib/term_frag_sel/fragmentation.py | 63 -----------
build/lib/term_frag_sel/utils.py | 46 --------
5 files changed, 2 insertions(+), 248 deletions(-)
delete mode 100644 build/lib/term_frag_sel/__init__.py
delete mode 100644 build/lib/term_frag_sel/cli.py
delete mode 100644 build/lib/term_frag_sel/fragmentation.py
delete mode 100644 build/lib/term_frag_sel/utils.py
diff --git a/.gitignore b/.gitignore
index 89a3870..67cda8e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -59,4 +59,5 @@ Temporary Items
__pycache__/
*_cache
*egg-info/
-.coverage
\ No newline at end of file
+.coverage
+build/
\ No newline at end of file
diff --git a/build/lib/term_frag_sel/__init__.py b/build/lib/term_frag_sel/__init__.py
deleted file mode 100644
index bb7d5f3..0000000
--- a/build/lib/term_frag_sel/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Initialise package."""
diff --git a/build/lib/term_frag_sel/cli.py b/build/lib/term_frag_sel/cli.py
deleted file mode 100644
index a9b8e95..0000000
--- a/build/lib/term_frag_sel/cli.py
+++ /dev/null
@@ -1,137 +0,0 @@
-"""Receive command line arguments, fragment sequences, and output fragments."""
-import argparse
-import logging
-from pathlib import Path
-from Bio import SeqIO # type: ignore
-import numpy as np
-import pandas as pd # type: ignore
-
-
-from term_frag_sel.fragmentation import fragmentation
-from term_frag_sel.utils import check_positive, check_prob
-
-
-def main(args: argparse.Namespace):
- """Use CLI arguments to fragment sequences and output text file \
- with selected terminal fragments.
-
- Args:
- args (parser): list of arguments from CLI.
- """
- # Create or wipe output file
- with open(args.output, "w", encoding="utf-8") as _:
- pass
-
- logger.info("Checking validity of files...")
- fasta, seq_counts = file_validation(args.fasta, args.counts, args.sep)
-
- logger.info("Fragmentation of %s...", args.fasta)
- fasta_parse = {}
- for record in fasta:
- fasta_parse[record.id] = record.seq
- splits = np.arange(0, len(list(fasta_parse))+args.size, args.size)
-
- for i, split in enumerate(splits):
- 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)
-
- logger.info("Writing batch %s sequences to %s...", i, args.output)
- with open(args.output, 'a', encoding="utf-8") as out_file:
- for line in term_frags:
- out_file.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", encoding="utf-8") as handle:
- fasta = SeqIO.parse(handle, "fasta")
- if not any(fasta):
- raise ValueError("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:
- argparse.Namespace: object of arguments from CLI.
- """
- parser = argparse.ArgumentParser(description="""Takes as input FASTA file
- 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,
- 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)")
- 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,
- type=check_prob,
- help="Probability cut happens after nucleotide A")
- 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,
- type=check_prob,
- help="Probability cut happens after nucleotide G")
- 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/build/lib/term_frag_sel/fragmentation.py b/build/lib/term_frag_sel/fragmentation.py
deleted file mode 100644
index 302fe6f..0000000
--- a/build/lib/term_frag_sel/fragmentation.py
+++ /dev/null
@@ -1,63 +0,0 @@
-"""Fragment sequences."""
-import re
-
-import numpy as np
-import pandas as pd # type: ignore
-
-
-def fragmentation(fasta: dict, seq_counts: pd.DataFrame,
- mean_length: int = 100, std: int = 10,
- a_prob: float = 0.22, t_prob: float = 0.25,
- g_prob: float = 0.25, c_prob: float = 0.28
- ) -> list:
- """Fragment cDNA sequences and select terminal fragment.
-
- Args:
- 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
- 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
- """
- # 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 = []
- 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)
-
- # 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()))
- for nuc in cut_nucs:
- nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
- pos = np.random.choice(nuc_pos)
- while pos in cuts:
- pos = np.random.choice(nuc_pos)
- cuts.append(pos)
-
- 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
- if term_frag != "":
- term_frags.append(term_frag)
-
- return term_frags
diff --git a/build/lib/term_frag_sel/utils.py b/build/lib/term_frag_sel/utils.py
deleted file mode 100644
index d77cc14..0000000
--- a/build/lib/term_frag_sel/utils.py
+++ /dev/null
@@ -1,46 +0,0 @@
-"""Utility functions for CLI arguments."""
-import argparse
-
-
-def check_positive(value: str) -> int:
- """Check input value is a positive integer.
-
- Args:
- value (str): 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: str) -> float:
- """Check probability value is within ]0,1] range.
-
- Args:
- value (str): 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("""Expected a positive float between
- 0 and 1, but got {value}""")
- return pvalue
--
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