-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Create
preprocess.input_formatter.py to summarize formatting functi…
…ons to a module.
- Loading branch information
Showing
2 changed files
with
123 additions
and
101 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| from __future__ import annotations | ||
|
|
||
| import uuid | ||
|
|
||
| from pathlib import Path | ||
| from typing import NamedTuple | ||
| from collections import defaultdict | ||
|
|
||
| from DAJIN2.utils import io, config, fastx_handler | ||
|
|
||
| from DAJIN2.core import preprocess | ||
|
|
||
|
|
||
| def parse_arguments(arguments: dict) -> tuple: | ||
| genome_urls = defaultdict(str) | ||
| if arguments.get("genome"): | ||
| genome_urls.update( | ||
| {"genome": arguments["genome"], "blat": arguments["blat"], "goldenpath": arguments["goldenpath"]} | ||
| ) | ||
|
|
||
| return ( | ||
| arguments["sample"], | ||
| arguments["control"], | ||
| arguments["allele"], | ||
| arguments["name"], | ||
| arguments["threads"], | ||
| genome_urls, | ||
| uuid.uuid4().hex, | ||
| ) | ||
|
|
||
|
|
||
| def convert_input_paths_to_posix(sample: str, control: str, allele: str) -> tuple: | ||
| sample = io.convert_to_posix(sample) | ||
| control = io.convert_to_posix(control) | ||
| allele = io.convert_to_posix(allele) | ||
|
|
||
| return sample, control, allele | ||
|
|
||
|
|
||
| def create_temporal_directory(name: str, control_name: str) -> Path: | ||
| tempdir = Path(config.TEMP_ROOT_DIR, name) | ||
| Path(tempdir, "cache", ".igvjs", control_name).mkdir(parents=True, exist_ok=True) | ||
|
|
||
| return tempdir | ||
|
|
||
|
|
||
| def check_caches(tempdir: Path, path_allele: str, genome_url: str) -> bool: | ||
| is_cache_hash = preprocess.exists_cached_hash(tempdir=tempdir, path=path_allele) | ||
| is_cache_genome = preprocess.exists_cached_genome(tempdir=tempdir, genome=genome_url) | ||
|
|
||
| return is_cache_hash and is_cache_genome | ||
|
|
||
|
|
||
| def get_genome_coordinates(genome_urls: dict, fasta_alleles: dict, is_cache_genome: bool, tempdir: Path) -> dict: | ||
| genome_coordinates = { | ||
| "genome": genome_urls["genome"], | ||
| "chrom_size": 0, | ||
| "chrom": "control", | ||
| "start": 0, | ||
| "end": len(fasta_alleles["control"]) - 1, | ||
| "strand": "+", | ||
| } | ||
| if genome_urls["genome"]: | ||
| if is_cache_genome: | ||
| genome_coordinates = next(io.read_jsonl(Path(tempdir, "cache", "genome_coordinates.jsonl"))) | ||
| else: | ||
| genome_coordinates = preprocess.fetch_coordinates( | ||
| genome_coordinates, genome_urls, fasta_alleles["control"] | ||
| ) | ||
| genome_coordinates["chrom_size"] = preprocess.fetch_chromosome_size( | ||
| genome_coordinates, genome_urls | ||
| ) | ||
| io.write_jsonl([genome_coordinates], Path(tempdir, "cache", "genome_coordinates.jsonl")) | ||
|
|
||
| return genome_coordinates | ||
|
|
||
|
|
||
| class FormattedInputs(NamedTuple): | ||
| path_sample: str | ||
| path_control: str | ||
| path_allele: str | ||
| sample_name: str | ||
| control_name: str | ||
| fasta_alleles: dict[str, str] | ||
| tempdir: Path | ||
| genome_coordinates: dict[str, str] | ||
| threads: int | ||
| uuid: str | ||
|
|
||
|
|
||
| def format_inputs(arguments: dict) -> FormattedInputs: | ||
| path_sample, path_control, path_allele, name, threads, genome_urls, uuid = parse_arguments(arguments) | ||
| path_sample, path_control, path_allele = convert_input_paths_to_posix(path_sample, path_control, path_allele) | ||
| sample_name = fastx_handler.extract_filename(path_sample) | ||
| control_name = fastx_handler.extract_filename(path_control) | ||
| fasta_alleles = fastx_handler.dictionize_allele(path_allele) | ||
| tempdir = create_temporal_directory(name, control_name) | ||
| is_cache_genome = check_caches(tempdir, path_allele, genome_urls["genome"]) | ||
| genome_coordinates = get_genome_coordinates(genome_urls, fasta_alleles, is_cache_genome, tempdir) | ||
|
|
||
| return FormattedInputs( | ||
| path_sample, | ||
| path_control, | ||
| path_allele, | ||
| sample_name, | ||
| control_name, | ||
| fasta_alleles, | ||
| tempdir, | ||
| genome_coordinates, | ||
| threads, | ||
| uuid, | ||
| ) |