diff --git a/src/momics/__init__.py b/src/momics/__init__.py index 9b01a81..2099262 100644 --- a/src/momics/__init__.py +++ b/src/momics/__init__.py @@ -14,7 +14,6 @@ from . import streamer from . import config from . import utils -from . import export from .version import __format_version__, __version__ __all__ = [ @@ -23,7 +22,6 @@ "streamer", "config", "utils", - "export", "__format_version__", "__version__", ] diff --git a/src/momics/cli/cp.py b/src/momics/cli/cp.py index 03a2f2c..ef100e3 100644 --- a/src/momics/cli/cp.py +++ b/src/momics/cli/cp.py @@ -1,7 +1,7 @@ import os import click -from .. import export, momics +from .. import momics from . import cli @@ -50,11 +50,11 @@ def cp(ctx, path, type, label, force, output): m = momics.Momics(path) if type == "sequence": - export.export_sequence(m, output) + m.export_sequence(output) elif type == "track": - export.export_track(m, label, output) + m.export_track(label, output) elif type == "features": - export.export_features(m, label, output) + m.export_features(label, output) else: return False diff --git a/src/momics/export.py b/src/momics/export.py deleted file mode 100644 index c2f9f71..0000000 --- a/src/momics/export.py +++ /dev/null @@ -1,91 +0,0 @@ -import logging -import os -from pathlib import Path -import numpy as np -import pyBigWig -import tiledb -import Bio -from Bio import SeqIO - -from .momics import Momics -from .momicsquery import MomicsQuery -from .utils import _check_feature_name, _check_track_name - - -def export_track(momics: Momics, track: str, output: Path) -> Momics: - """Export a track from a `.momics` repository as a `.bw `file. - - Args: - track (str): Which track to remove - output (Path): Prefix of the output bigwig file - - Returns: - Momics: An updated Momics object - """ - # Abort if `track` is not listed - _check_track_name(track, momics.tracks()) - - # Silence logger - logging.disable(logging.CRITICAL) - - # Init output file - bw = pyBigWig.open(output, "w") - chrom_sizes = momics.chroms()[["chrom", "length"]].apply(tuple, axis=1).tolist() - bw.addHeader(chrom_sizes) - for chrom, chrom_length in chrom_sizes: - tdb = momics._build_uri("coverage", f"{chrom}.tdb") - with tiledb.open(tdb, "r", ctx=momics.cfg.ctx) as A: - values0 = A.query(attrs=[track])[:][track][:-1] - chroms = np.array([chrom] * chrom_length) - starts = np.array(range(chrom_length)) - ends = starts + 1 - bw.addEntries(chroms, starts=starts, ends=ends, values=values0) - bw.close() - - return momics - - -def export_sequence(momics: Momics, output: Path) -> Momics: - """Export sequence from a `.momics` repository as a `.fa `file. - - Args: - output (Path): Prefix of the output bigwig file - - Returns: - Momics: An updated Momics object - """ - # Silence logger - logging.disable(logging.CRITICAL) - - if os.path.exists(output): - os.remove(output) - - # Init output file - chroms = momics.chroms()["chrom"] - with open(output, "a") as output_handle: - for chrom in chroms: - q = MomicsQuery(momics, chrom).query_sequence() - seq = q.seq["nucleotide"][next(iter(q.seq["nucleotide"].keys()))] # type: ignore - sr = Bio.SeqRecord.SeqRecord(Bio.Seq.Seq(seq), id=chrom, description="") - SeqIO.write(sr, output_handle, "fasta") - - return momics - - -def export_features(momics: Momics, features: str, output: Path) -> Momics: - """Export a features set from a `.momics` repository as a `.bed `file. - - Args: - features (str): Which features to remove - output (Path): Prefix of the output BED file - - Returns: - Momics: An updated Momics object - """ - # Abort if `features` is not listed - _check_feature_name(features, momics.features()) - - # Init output file - bed = momics.features(features) - bed.to_bed(output) - return momics diff --git a/src/momics/momics.py b/src/momics/momics.py index 08b7185..5e4cf97 100644 --- a/src/momics/momics.py +++ b/src/momics/momics.py @@ -1,4 +1,5 @@ import concurrent.futures +import logging import os import tempfile import multiprocessing @@ -7,6 +8,8 @@ from datetime import datetime from pathlib import Path from typing import Dict, Literal, Optional, Union +import Bio +from Bio import SeqIO import numpy as np import pandas as pd @@ -871,3 +874,75 @@ def remove_directory_until_success(vfs, dir_uri, max_retries=10, retry_delay=2): remove_directory_until_success(vfs, self.path) return True + + def export_track(self, track: str, output: Path) -> "Momics": + """Export a track from a `.momics` repository as a `.bw `file. + + Args: + track (str): Which track to remove + output (Path): Prefix of the output bigwig file + + Returns: + Momics: An updated Momics object + """ + # Abort if `track` is not listed + utils._check_track_name(track, self.tracks()) + + # Init output file + bw = pyBigWig.open(output, "w") + chrom_sizes = self.chroms()[["chrom", "length"]].apply(tuple, axis=1).tolist() + bw.addHeader(chrom_sizes) + for chrom, chrom_length in chrom_sizes: + tdb = self._build_uri("coverage", f"{chrom}.tdb") + with tiledb.open(tdb, "r", ctx=self.cfg.ctx) as A: + values0 = A.query(attrs=[track])[:][track][:-1] + chroms = np.array([chrom] * chrom_length) + starts = np.array(range(chrom_length)) + ends = starts + 1 + bw.addEntries(chroms, starts=starts, ends=ends, values=values0) + bw.close() + + return self + + def export_sequence(self, output: Path) -> "Momics": + """Export sequence from a `.momics` repository as a `.fa `file. + + Args: + output (Path): Prefix of the output bigwig file + + Returns: + Momics: An updated Momics object + """ + # Silence logger + logging.disable(logging.CRITICAL) + + if os.path.exists(output): + os.remove(output) + + # Init output file + chroms = self.chroms()["chrom"] + with open(output, "a") as output_handle: + for chrom in chroms: + seq = self.seq(chrom) + sr = Bio.SeqRecord.SeqRecord(Bio.Seq.Seq(seq), id=chrom, description="") + SeqIO.write(sr, output_handle, "fasta") + + return self + + def export_features(self, features: str, output: Path) -> "Momics": + """Export a features set from 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3472804..d7d9db9 100644 --- a/tests/test_track_export.py +++ b/tests/test_track_export.py @@ -4,7 +4,6 @@ import pytest from momics import momics -from momics.export import export_track, export_sequence, export_features @pytest.mark.order(999) @@ -12,12 +11,12 @@ def test_export(momics_path: str): p = tempfile.NamedTemporaryFile().name mom = momics.Momics(momics_path) print(mom.tracks()) - export_track(mom, "bw2", p) + mom.export_track("bw2", p) assert os.path.exists(p) os.remove(p) - export_sequence(mom, p) + mom.export_sequence(p) assert os.path.exists(p) os.remove(p) - export_features(mom, "ft1", p) + mom.export_features("ft1", p) assert os.path.exists(p) os.remove(p)