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a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ![](example/diagram.png) -[See more example](https://sashimi.readthedocs.io/en/latest/) +[Tutorials](https://sashimi.readthedocs.io/en/latest/) ## what is sashimi.py diff --git a/requirements.txt b/requirements.txt index e7209a0..707ec63 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,51 +1,47 @@ asciitree>=0.3.3 cairocffi>=1.4.0 -certifi>=2022.9.24 +certifi>=2022.9.24 ; python_version >= '3.6' cffi>=1.15.1 -charset-normalizer>=2.1.1 +charset-normalizer>=2.1.1 ; python_full_version >= '3.6.0' click>=8.1.3 -click-option-group>=0.5.3 -contourpy>=1.0.5 +click-option-group>=0.5.5 +contourpy>=1.0.6 ; python_version >= '3.7' cooler>=0.8.11 -cycler>=0.11.0 +cycler>=0.11.0 ; python_version >= '3.6' cytoolz>=0.10.1 -dill>=0.3.5.1 -filetype>=1.1.0 -fonttools>=4.37.3 -h5py>=3.7.0 +dill>=0.3.6 ; python_version >= '3.7' +filetype>=1.2.0 +fonttools>=4.38.0 ; python_version >= '3.7' +h5py>=3.7.0 ; python_version >= '3.7' hicmatrix>=15 -idna>=3.4 +idna>=3.4 ; python_version >= '3.5' intervaltree>=3.1.0 -kiwisolver>=1.4.4 +kiwisolver>=1.4.4 ; python_version >= '3.7' loguru>=0.6.0 -matplotlib>=3.6.0 -multiprocess>=0.70.13 -numexpr>=2.8.3 -numpy>=1.23.3 -packaging>=21.3 -pandas>=1.5.0 -pillow>=9.2.0 +matplotlib>=3.6.2 +multiprocess>=0.70.14 ; python_version >= '3.7' +numexpr>=2.8.4 ; python_version >= '3.7' +numpy>=1.23.4 +packaging>=21.3 ; python_version >= '3.6' +pandas>=1.5.1 +pillow>=9.3.0 ; python_version >= '3.7' pybigwig>=0.3.18 pycparser>=2.21 pyfaidx>=0.7.1 pypairix>=0.3.7 -pyparsing>=3.0.9 -pysam>=0.19.1 -python-dateutil>=2.8.2 -pytz>=2022.2.1 -pyyaml>=6.0 +pyparsing>=3.0.9 ; python_full_version >= '3.6.8' +pysam>=0.20.0 +python-dateutil>=2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' +pytz>=2022.6 +pyyaml>=6.0 ; python_version >= '3.6' requests>=2.28.1 -scipy>=1.9.1 -seaborn>=0.12.0 -setuptools>=65.4.0 -simplejson>=3.17.6 -six>=1.16.0 +scipy>=1.9.3 +seaborn>=0.12.1 +setuptools>=65.5.1 ; python_version >= '3.7' +simplejson>=3.18.0 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3' +six>=1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' sortedcontainers>=2.4.0 -tables>=3.7.0 -toolz>=0.12.0 -urllib3>=1.26.12 +tables>=3.7.0 ; python_version >= '3.6' +toolz>=0.12.0 ; python_version >= '3.5' +urllib3>=1.26.12 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4' xmltodict>=0.13.0 - -uvicorn~=0.18.2 -fastapi~=0.79.0 -pydantic~=1.9.1 \ No newline at end of file diff --git a/sashimi/base/ReadDepth.py b/sashimi/base/ReadDepth.py index 63a92d1..18f4ae1 100644 --- a/sashimi/base/ReadDepth.py +++ b/sashimi/base/ReadDepth.py @@ -47,7 +47,6 @@ def __init__(self, self.junctions_dict = junctions_dict self.strand_aware = strand_aware self.minus = abs(minus) if minus is not None else minus - self.max = max(self.wiggle, default=0) self.junction_dict_plus = junction_dict_plus self.junction_dict_minus = junction_dict_minus self.site_plus = site_plus @@ -55,7 +54,7 @@ def __init__(self, @property def wiggle(self) -> np.array: - if (self.plus is None or np.sum(self.plus) == 0) and self.minus is not None: + if (self.plus is None or not self.plus.any()) and self.minus is not None: return self.minus if self.plus is not None and self.minus is not None: @@ -63,6 +62,10 @@ def wiggle(self) -> np.array: return self.plus + @property + def max(self) -> float: + return max(self.wiggle, default=0) + def __add__(self, other): """ @@ -74,28 +77,33 @@ def __add__(self, other): A new ReadDepth object containing the sum of the two original ReadDepth objects """ - if len(self.wiggle) == len(other.wiggle): - junctions = self.junctions_dict if self.junctions_dict else {} - if other.junctions_dict: - for i, j in other.junctions_dict.items(): - if i in junctions.keys(): - junctions[i] += j - else: - junctions[i] = j - - minus = None - if self.minus is not None and other.minus is not None: - minus = self.minus + other.minus - elif self.minus is None and other.minus is not None: - minus = other.minus - elif self.minus is not None and other.minus is None: - minus = self.minus - - return ReadDepth( - self.plus + other.plus, - junctions_dict=junctions, - minus=minus - ) + if self.wiggle is not None and other.wiggle is not None: + if len(self.wiggle) == len(other.wiggle): + junctions = self.junctions_dict if self.junctions_dict else {} + if other.junctions_dict: + for i, j in other.junctions_dict.items(): + if i in junctions.keys(): + junctions[i] += j + else: + junctions[i] = j + + minus = None + if self.minus is not None and other.minus is not None: + minus = self.minus + other.minus + elif self.minus is None and other.minus is not None: + minus = other.minus + elif self.minus is not None and other.minus is None: + minus = self.minus + + return ReadDepth( + self.plus + other.plus, + junctions_dict=junctions, + minus=minus + ) + elif self.wiggle is None: + return other + else: + return self def curr_height(self, pos: int) -> float: if self.minus is None: diff --git a/sashimi/cli.py b/sashimi/cli.py index d6a4850..bee9c0f 100644 --- a/sashimi/cli.py +++ b/sashimi/cli.py @@ -21,7 +21,7 @@ from sashimi.file.ATAC import ATAC from sashimi.plot import Plot -__version__ = "0.0.6" +__version__ = "0.0.7" __author__ = "ygidtu & Ran Zhou" __email__ = "ygidtu@gmail.com" @@ -49,6 +49,9 @@ def __init__(self, library: str = "fru", trans: Optional[str] = None, depth: int = 30000): + + if path.startswith("~"): + path = os.path.expanduser(path) self.path = os.path.abspath(path) if not os.path.exists(self.path): @@ -63,6 +66,10 @@ def __init__(self, self.trans = trans self.depth = depth + @property + def name(self) -> str: + return os.path.basename(self.path) + def __str__(self): return f"path: {self.path} \nlabel: {self.label} \ngroup: {self.group} \n" \ f"color: {self.color} \ncategory: {self.category} \nlibrary: {self.library}" @@ -114,7 +121,7 @@ def __read_iter__(path): def process_file_list(infile: str, category: str = "density"): u""" - Process and check the file list format + Process and check the file list format_ :param infile: path to input file list :param category: the image type of file list used for """ @@ -235,7 +242,7 @@ def process_file_list(infile: str, category: str = "density"): show_default=True) @optgroup.option("--barcode", type=click.Path(exists=True), show_default=True, help="Path to barcode list file, At list two columns were required, " - "- 1st The name of bam file; \b" + "- 1st The name of bam file, not the alias of bam; \b" "- 2nd the barcode; \b" "- 3rd The group label, optional; \b" "- 4th The color of each cell type, default using the color of corresponding bam file.\n") @@ -519,8 +526,8 @@ def main(**kwargs): p.add_interval(f.path, f.label) elif key == "density": for f in process_file_list(kwargs[key], key): - if barcodes and f.label in barcodes.keys() and f.category in ["bam", "atac"]: - for group in barcodes[f.label].keys(): + if barcodes and f.name in barcodes.keys() and f.category in ["bam", "atac"]: + for group in barcodes[f.name].keys(): if kwargs["group_by_cell"] and group: label = group elif group: @@ -530,13 +537,13 @@ def main(**kwargs): if f.label not in size_factors.keys() and f.category == "atac": logger.info(f"Indexing {f.path}") - size_factors[f.label] = ATAC.index(f.path, barcodes[f.label]) + size_factors[f.label] = ATAC.index(f.path, barcodes[f.name]) p.add_density(f.path, category=f.category, label=label, barcode=group, - barcode_groups=barcodes[f.label], + barcode_groups=barcodes[f.name], barcode_tag=kwargs["barcode_tag"], umi_tag=kwargs["umi_tag"], library=f.library, @@ -568,17 +575,17 @@ def main(**kwargs): density_by_strand=kwargs["density_by_strand"],) elif key == "heatmap": for f in process_file_list(kwargs[key], key): - if barcodes and f.label in barcodes.keys() and f.category in ["bam", "atac"]: + if barcodes and f.name in barcodes.keys() and f.category in ["bam", "atac"]: if f.label not in size_factors.keys() and f.category == "atac": logger.info(f"Indexing {f.path}") - size_factors[f.label] = ATAC.index(f.path, barcodes[f.label]) + size_factors[f.label] = ATAC.index(f.path, barcodes[f.name]) - for group in barcodes[f.label].keys(): + for group in barcodes[f.name].keys(): p.add_heatmap(f.path, category=f.category, label=f"{f.label} - {group}" if group else f.label, barcode=group, - barcode_groups=barcodes[f.label], + barcode_groups=barcodes[f.name], group=f"{f.group} - {group}" if f.group else f.group, barcode_tag=kwargs["barcode_tag"], size_factor=size_factors.get(f.label), @@ -613,8 +620,8 @@ def main(**kwargs): vmax=kwargs["heatmap_vmax"]) elif key == "line": for f in process_file_list(kwargs[key], key): - if barcodes and f.label in barcodes.keys() and f.category == "bam": - for group in barcodes[f.label].keys(): + if barcodes and f.name in barcodes.keys() and f.category == "bam": + for group in barcodes[f.name].keys(): if kwargs["group_by_cell"] and group: label = group elif group: @@ -732,7 +739,8 @@ def main(**kwargs): "density": kwargs["sc_density_height_ratio"] }, distance_between_label_axis=kwargs["distance_ratio"], - included_junctions=included_junctions + included_junctions=included_junctions, + n_jobs=kwargs.get("process", 1) ) diff --git a/sashimi/file/File.py b/sashimi/file/File.py index a9f8055..991893e 100644 --- a/sashimi/file/File.py +++ b/sashimi/file/File.py @@ -38,6 +38,9 @@ def end(self) -> int: def load(self, *args, **kwargs): return None + def len(self, scale=1) -> int: + return len(self.data) / scale if self.data else 0 + def __hash__(self) -> int: return hash((self.path, self.label, self.title)) diff --git a/sashimi/file/Reference.py b/sashimi/file/Reference.py index 5d4f4e9..9fd967b 100644 --- a/sashimi/file/Reference.py +++ b/sashimi/file/Reference.py @@ -13,7 +13,6 @@ from typing import List, Union, Optional import filetype -import matplotlib as mpl import pysam from loguru import logger @@ -22,7 +21,6 @@ from sashimi.base.Readder import Reader from sashimi.base.Transcript import Transcript from sashimi.file.File import File -from sashimi.base.CoordinateMap import Coordinate class Reference(File): @@ -133,9 +131,7 @@ def __load_local_domain__(self, region: GenomicLoci): for record in Reader.read_bigbed(bb_file, region): record = record[2].split("\t") current_id = record[0] - strand = record[2] current_start = int(record[3]) - num_of_chunk = record[6] block_sizes = [int(x) for x in record[7].split(",") if x] block_starts = [int(x) for x in record[8].split(",") if x] current_desc = record[17] @@ -307,7 +303,6 @@ def index_gtf(cls, input_gtf): gtf = cls.is_gtf(input_gtf) assert gtf % 10 == 1, f"{input_gtf} seems not be gtf format" - index = False if gtf // 10 > 0: output_gtf = input_gtf else: @@ -369,11 +364,10 @@ def __load_gtf__(self, region: GenomicLoci) -> List[Transcript]: strand=rec.strand, transcript_id=rec.transcript_id, gene_id=rec.gene_id, - gene=rec.gene_name, - transcript=rec.transcript_name, + gene=rec.gene_name if "gene_name" in rec.attributes else "", + transcript=rec.transcript_name if "transcript_name" in rec.attributes else "", exons=[] ) - elif re.search(r"(exon)", rec.feature, re.I): if rec.transcript_id not in exons.keys(): exons[rec.transcript_id] = [] @@ -444,12 +438,11 @@ def __load_bam__(self, region: GenomicLoci, threshold_of_reads: int = 0) -> List return sorted([x for x, y in transcripts.items() if y > threshold_of_reads]) - def __load_bed__(self, region: GenomicLoci)-> List[Transcript]: + def __load_bed__(self, region: GenomicLoci) -> List[Transcript]: transcripts = [] try: for rec in Reader.read_gtf(self.path, region=region, bed=True): exon_bound = [] - intron_bound = [] current_start = int(rec[1]) current_end = int(rec[2]) if len(rec) > 3: @@ -525,6 +518,7 @@ def load(self, region: GenomicLoci, threshold_of_reads: int = 0, **kwargs): elif self.category == "bed": self.data = self.__load_bed__(region) + rec, start, end, strand = None, None, None, None for interval_file, interval_label in self.interval_file.items(): try: if not os.path.exists(interval_file + ".tbi"): @@ -562,7 +556,7 @@ def load(self, region: GenomicLoci, threshold_of_reads: int = 0, **kwargs): ) ) - if len(interval_target) != 0: + if len(interval_target) != 0 and rec is not None: self.data.append(Transcript( chromosome=rec.contig, start=start, diff --git a/sashimi/plot.py b/sashimi/plot.py index bddea90..3f97608 100644 --- a/sashimi/plot.py +++ b/sashimi/plot.py @@ -5,7 +5,7 @@ """ import io import logging -import os.path +import os from typing import Set import matplotlib.pyplot as plt @@ -381,6 +381,7 @@ def __init_input_file__(path: str, # for ATAC size_factor=None ): + path = os.path.expanduser(path) if category == "bam": obj = Bam.create( path, @@ -597,8 +598,10 @@ def add_heatmap(self, 'pink', 'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia', 'hot', 'afmhot', 'gist_heat', 'copper' :param show_row_names: - :param vmin: Values to anchor the colormap, otherwise they are inferred from the data and other keyword arguments. - :param vmax: Values to anchor the colormap, otherwise they are inferred from the data and other keyword arguments. + :param vmin: Values to anchor the colormap, + otherwise they are inferred from the data and other keyword arguments. + :param vmax: Values to anchor the colormap, + otherwise they are inferred from the data and other keyword arguments. :return: """ obj, category = self.__init_input_file__( @@ -923,6 +926,7 @@ def plot(self, return_image: Optional[str] = None, sc_height_ratio: Optional[Dict[str, float]] = None, distance_between_label_axis: float = .3, + n_jobs: int = 1, *args, **kwargs): u""" draw image @@ -935,6 +939,7 @@ def plot(self, :param raster: plot rasterizer site plot :param sc_height_ratio: adjust the relative height of single cell plots :param distance_between_label_axis: distance between y-axis label and y-axis ticks + :param n_jobs: load data in how many processes :param return_image: used for interactive ui """ if sc_height_ratio is None: @@ -965,7 +970,8 @@ def plot(self, assert isinstance(p, PlotInfo), f"unrecognized data type: {type(p)}" try: p.load(region=self.region if p.type != "motif" else self.params[p]["region"], - junctions=self.junctions.get(p.obj[0].label, {}), *args, **kwargs) + junctions=self.junctions.get(p.obj[0].label, {}), + n_jobs=n_jobs, *args, **kwargs) except Exception as err: logger.warning(f"failed to load data from {p}") raise err diff --git a/server.py b/server.py index 36869ac..b69c5f8 100644 --- a/server.py +++ b/server.py @@ -5,7 +5,6 @@ """ import inspect -import os import pickle import sys import traceback diff --git a/setup.py b/setup.py index 2b42abb..a114101 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ import os from setuptools import setup, find_packages -__version__ = "0.0.6" +__version__ = "0.0.7" __author__ = "ygidtu & Ran Zhou" __email__ = "ygidtu@gmail.com" diff --git a/web/package.json b/web/package.json index 2e051d8..aaf660b 100644 --- a/web/package.json +++ b/web/package.json @@ -1,7 +1,7 @@ { "name": "sashimi.py", "private": true, - "version": "0.0.6", + "version": "0.0.7", "type": "module", "scripts": { "dev": "vite",