From 965e3e5cbdf4e88a7163d14a033e2a11ae6352b5 Mon Sep 17 00:00:00 2001 From: js2264 Date: Mon, 21 Oct 2024 11:10:04 +0200 Subject: [PATCH] feat: API change: mv export_* to momics methods --- src/momics/__init__.py | 2 - src/momics/cli/cp.py | 8 +- src/momics/export.py | 91 ------------------ src/momics/momics.py | 75 +++++++++++++++ testCLI.mom/__tiledb_group.tdb | 0 ...14_7a01072c147c28356ba1667e3cda56cb_22.wrt | 0 ...77_3a4e54214b29ce35291b206f610415ff_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 6725 bytes .../a0.tdb | Bin 0 -> 4020 bytes .../a1.tdb | Bin 0 -> 1544 bytes .../a1_var.tdb | Bin 0 -> 1020 bytes .../a2.tdb | Bin 0 -> 1544 bytes .../a2_var.tdb | Bin 0 -> 1020 bytes .../d0.tdb | Bin 0 -> 55 bytes .../d1.tdb | Bin 0 -> 1231 bytes .../d2.tdb | Bin 0 -> 1230 bytes .../__fragment_metadata.tdb | Bin 0 -> 6742 bytes .../a0.tdb | Bin 0 -> 4024 bytes .../a1.tdb | Bin 0 -> 1545 bytes .../a1_var.tdb | Bin 0 -> 1021 bytes .../a2.tdb | Bin 0 -> 1545 bytes .../a2_var.tdb | Bin 0 -> 1021 bytes .../d0.tdb | Bin 0 -> 2063 bytes .../d1.tdb | Bin 0 -> 1233 bytes .../d2.tdb | Bin 0 -> 1232 bytes ...501803061_261a14f3e08e67342f6bbfc4fbc6242c | Bin 0 -> 233 bytes ...30_061881b396f49aea1623743416bd9345_22.wrt | 0 ...93_2b48012cb6878e463fd06d735d68e10c_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 6729 bytes .../a0.tdb | Bin 0 -> 20020 bytes .../a1.tdb | Bin 0 -> 5740 bytes .../a1_var.tdb | Bin 0 -> 5020 bytes .../a2.tdb | Bin 0 -> 5740 bytes .../a2_var.tdb | Bin 0 -> 5020 bytes .../d0.tdb | Bin 0 -> 56 bytes .../d1.tdb | Bin 0 -> 5632 bytes .../d2.tdb | Bin 0 -> 5630 bytes .../__fragment_metadata.tdb | Bin 0 -> 6746 bytes .../a0.tdb | Bin 0 -> 20024 bytes .../a1.tdb | Bin 0 -> 5741 bytes .../a1_var.tdb | Bin 0 -> 5021 bytes .../a2.tdb | Bin 0 -> 5741 bytes .../a2_var.tdb | Bin 0 -> 5021 bytes .../d0.tdb | Bin 0 -> 10064 bytes .../d1.tdb | Bin 0 -> 5633 bytes .../d2.tdb | Bin 0 -> 5631 bytes ...501803062_69298f836cb6d3a193a102a4a450dc67 | Bin 0 -> 235 bytes ...49_7fd88dcdbc493f0e64fdba34429544c5_22.wrt | 0 ...09_5b33ff6dae2a413b47e5904df9e15320_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 6728 bytes .../a0.tdb | Bin 0 -> 12020 bytes .../a1.tdb | Bin 0 -> 3670 bytes .../a1_var.tdb | Bin 0 -> 3020 bytes .../a2.tdb | Bin 0 -> 3670 bytes .../a2_var.tdb | Bin 0 -> 3020 bytes .../d0.tdb | Bin 0 -> 55 bytes .../d1.tdb | Bin 0 -> 3432 bytes .../d2.tdb | Bin 0 -> 3430 bytes .../__fragment_metadata.tdb | Bin 0 -> 6747 bytes .../a0.tdb | Bin 0 -> 12024 bytes .../a1.tdb | Bin 0 -> 3671 bytes .../a1_var.tdb | Bin 0 -> 3021 bytes .../a2.tdb | Bin 0 -> 3671 bytes .../a2_var.tdb | Bin 0 -> 3021 bytes .../d0.tdb | Bin 0 -> 6064 bytes .../d1.tdb | Bin 0 -> 3433 bytes .../d2.tdb | Bin 0 -> 3431 bytes ...501803064_4ce2f6fc0230a01db27afe8f78ed7136 | Bin 0 -> 234 bytes ...65_19262b94897652646185dc96aa9f5eda_22.wrt | 0 ...26_414dcc3a8a0751338e5c428884b2e7ba_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 6728 bytes .../a0.tdb | Bin 0 -> 16024 bytes .../a1.tdb | Bin 0 -> 4710 bytes .../a1_var.tdb | Bin 0 -> 4021 bytes .../a2.tdb | Bin 0 -> 4710 bytes .../a2_var.tdb | Bin 0 -> 4021 bytes .../d0.tdb | Bin 0 -> 55 bytes .../d1.tdb | Bin 0 -> 4533 bytes .../d2.tdb | Bin 0 -> 4531 bytes .../__fragment_metadata.tdb | Bin 0 -> 6745 bytes .../a0.tdb | Bin 0 -> 16028 bytes .../a1.tdb | Bin 0 -> 4711 bytes .../a1_var.tdb | Bin 0 -> 4022 bytes .../a2.tdb | Bin 0 -> 4711 bytes .../a2_var.tdb | Bin 0 -> 4022 bytes .../d0.tdb | Bin 0 -> 8066 bytes .../d1.tdb | Bin 0 -> 4534 bytes .../d2.tdb | Bin 0 -> 4532 bytes ...501803065_69a02bd24b62a77c5ed8f3f81ae1e49c | Bin 0 -> 235 bytes testCLI.mom/annotations/__tiledb_group.tdb | 0 ...85_4e9917e80c42c37deae90ceac2e3323b_22.wrt | 0 ...46_5ccc84b8798031e9aa6de61798180c8f_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4021 bytes .../a0.tdb | Bin 0 -> 53 bytes .../a0_var.tdb | Bin 0 -> 24 bytes .../a1.tdb | Bin 0 -> 28 bytes .../__fragment_metadata.tdb | Bin 0 -> 4021 bytes .../a0.tdb | Bin 0 -> 53 bytes .../a0_var.tdb | Bin 0 -> 24 bytes .../a1.tdb | Bin 0 -> 28 bytes ...501803056_20a0ada741a1d52959a23e945f405d6a | Bin 0 -> 183 bytes ...85_1d6fd68139aefd9f8e0f9538545754e6_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4028 bytes .../a0.tdb | Bin 0 -> 127 bytes .../a1.tdb | Bin 0 -> 127 bytes ...501802666_538ab1b64fe53f17d8658b9cff0368a3 | Bin 0 -> 186 bytes ...501802678_61dfca13a9e0d9ef8285f651ef302ea8 | Bin 0 -> 197 bytes ...501802680_6773373afaaa297f0a8d45cee1456089 | Bin 0 -> 180 bytes ...501802682_11e8d7a9da309c32159bb8d5391c099b | Bin 0 -> 187 bytes ...99_14b3f2aeb1318424e5a987806a60626f_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4068 bytes .../a0.tdb | Bin 0 -> 548 bytes .../a1.tdb | Bin 0 -> 548 bytes ...501802668_0fda766e2fef13388e95bcbd6dc794d1 | Bin 0 -> 188 bytes ...501802692_2dcd83db496f2cf60facf6798cc611d4 | Bin 0 -> 199 bytes ...501802693_618742ef5d7ae46e05df233253a2a721 | Bin 0 -> 182 bytes ...501802695_5b03fe9a3da862eb52d7a9d89c7001a0 | Bin 0 -> 188 bytes ...12_5c3d2c1918e0f346231482ceafcaba1d_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4026 bytes .../a0.tdb | Bin 0 -> 308 bytes .../a1.tdb | Bin 0 -> 308 bytes ...501802669_6f600108243f83e07e24794d6402bd65 | Bin 0 -> 187 bytes ...501802706_2cb8e2d8e6fa2553ae19ee99e7f1d000 | Bin 0 -> 198 bytes ...501802707_7ba59173cae705519d47c9acf668f5e0 | Bin 0 -> 181 bytes ...501802709_16849fd1aa7363e8e74a50c29a8c0125 | Bin 0 -> 187 bytes ...26_06111d64a6952c4a546005c69b847451_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4070 bytes .../a0.tdb | Bin 0 -> 481 bytes .../a1.tdb | Bin 0 -> 481 bytes ...501802671_14e09398a42ee9d1868d01f5172f44c4 | Bin 0 -> 188 bytes ...501802719_362105370a032b874ca9b9134cf97156 | Bin 0 -> 199 bytes ...501802721_03398fb31e2ee32d04a50a9505da2cf8 | Bin 0 -> 182 bytes ...501802723_01cb508ee892358ce978e250f2c3b822 | Bin 0 -> 188 bytes testCLI.mom/coverage/__tiledb_group.tdb | 0 ...50_5fbbeb7afd62894098b10b8188ad2997_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4127 bytes .../a0.tdb | Bin 0 -> 106 bytes .../a0_var.tdb | Bin 0 -> 46 bytes .../a1.tdb | Bin 0 -> 106 bytes .../a1_var.tdb | Bin 0 -> 104 bytes ...501802662_7a94ede4d7b1ea93a99275745657ca4d | Bin 0 -> 182 bytes ...83_0d6b634f769d5bfa051651eb1f07014b_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 3092 bytes .../a0.tdb | Bin 0 -> 10923 bytes .../a0_var.tdb | Bin 0 -> 3308 bytes ...501802870_366c6d4234b9ec02a144a3e798a5d6e9 | Bin 0 -> 180 bytes ...02_6e0253cc0fe1ac62979fdd535be69d73_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 3099 bytes .../a0.tdb | Bin 0 -> 66734 bytes .../a0_var.tdb | Bin 0 -> 15810 bytes ...501802872_0a5fe3ce0cecf905a45d55ddc241ce6f | Bin 0 -> 182 bytes ...18_2ebe2c13a1fb80b04347e24c716495e0_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 3092 bytes .../a0.tdb | Bin 0 -> 31343 bytes .../a0_var.tdb | Bin 0 -> 9461 bytes ...501802873_470db400a6a1c529373d6be26e1f5a3f | Bin 0 -> 181 bytes ...36_108c4fb8b698ff4167c40fbf7b859812_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 3099 bytes .../a0.tdb | Bin 0 -> 66734 bytes .../a0_var.tdb | Bin 0 -> 12661 bytes ...501802875_525537b1303c9a3ea332f095afab8860 | Bin 0 -> 182 bytes testCLI.mom/genome/__tiledb_group.tdb | 0 ...24_6068993d5e2a9744a77cc0f53c33d69f_22.wrt | 0 .../__fragment_metadata.tdb | Bin 0 -> 4014 bytes .../a0.tdb | Bin 0 -> 66 bytes .../a0_var.tdb | Bin 0 -> 28 bytes .../a1.tdb | Bin 0 -> 52 bytes ...501802624_6068993c63827e4d7578430e952f47d3 | Bin 0 -> 213 bytes ...501802619_10418e4d9f8c591689ea48860ddded82 | Bin 0 -> 193 bytes tests/test_track_export.py | 7 +- 170 files changed, 82 insertions(+), 101 deletions(-) delete mode 100644 src/momics/export.py create mode 100644 testCLI.mom/__tiledb_group.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__commits/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22.wrt create mode 100644 testCLI.mom/annotations/I.tdb/__commits/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22.wrt create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/__fragment_metadata.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/a0.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/a1.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/a1_var.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/a2.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/a2_var.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/d0.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/d1.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803114_1729501803114_7a01072c147c28356ba1667e3cda56cb_22/d2.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/__fragment_metadata.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/a0.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/a1.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/a1_var.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/a2.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/a2_var.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/d0.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/d1.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__fragments/__1729501803377_1729501803377_3a4e54214b29ce35291b206f610415ff_22/d2.tdb create mode 100644 testCLI.mom/annotations/I.tdb/__schema/__1729501803061_1729501803061_261a14f3e08e67342f6bbfc4fbc6242c create mode 100644 testCLI.mom/annotations/II.tdb/__commits/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22.wrt create mode 100644 testCLI.mom/annotations/II.tdb/__commits/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22.wrt create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/__fragment_metadata.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/a0.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/a1.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/a1_var.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/a2.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/a2_var.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/d0.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/d1.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803130_1729501803130_061881b396f49aea1623743416bd9345_22/d2.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22/__fragment_metadata.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22/a0.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22/a1.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22/a1_var.tdb create mode 100644 testCLI.mom/annotations/II.tdb/__fragments/__1729501803393_1729501803393_2b48012cb6878e463fd06d735d68e10c_22/a2.tdb create mode 100644 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"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 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 + utils._check_feature_name(features, self.features()) + + # Init output file + bed = self.features(features) + 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@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)