brie 2.3.0__tar.gz → 2.3.1__tar.gz

brie-2.3.1/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # required for trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build
+        run: pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

brie-2.3.1/.gitignore

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+.DS_Store*
+.vscode/
+temp/
+doc/*.ipynb
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+

brie-2.3.1/.gitmodules

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+[submodule "brie-tutorials"]
+	path = brie-tutorials
+	url = https://github.com/huangyh09/brie-tutorials

brie-2.3.1/.readthedocs.yml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: doc/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+    install:
+    - requirements: doc/requirements.txt

brie-2.3.1/.travis.yml

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+
+language: python
+python:
+  - "3.6"
+  - "3.7"
+cache: pip
+install:
+  - pip install pysam
+script:
+  - python setup.py check

brie-2.3.1/MANIFEST.in

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+include requirements.txt
+include README.rst

{brie-2.3.0 → brie-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: brie
-Version: 2.3.0
+Version: 2.3.1
 Summary: BRIE: Bayesian regression for isoform estimate
 Home-page: https://brie.readthedocs.io
 Author: Yuanhua Huang

brie-2.3.1/brie/version.py

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+__version__ = "2.3.1"
+

brie-2.3.1/brie/version1/brie.py

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+# This is a main file to run the diceseq software, which will return the 
+# isoform proportions ratio for each gene at all time points.
+
+import os
+import sys
+import time
+import pysam
+import numpy as np
+import multiprocessing
+from optparse import OptionParser, OptionGroup
+
+# import pyximport; pyximport.install()
+from ..utils.gtf_utils import load_genes
+from ..utils.run_utils import set_info, map_data, save_data
+from .model_brie import brie_MH_Heuristic
+
+PROCESSED = 0
+TOTAL_GENE = 0
+TOTAL_READ = []
+START_TIME = time.time()
+    
+def show_progress(RV=None):
+    global PROCESSED, TOTAL_GENE, START_TIME
+    if RV is not None: 
+        PROCESSED += 1
+        bar_len = 20
+        run_time = time.time() - START_TIME
+        percents = 100.0 * PROCESSED / TOTAL_GENE
+        filled_len = int(bar_len * percents / 100)
+        bar = '=' * filled_len + '-' * (bar_len - filled_len)
+        
+        sys.stdout.write('\r[Brie] [%s] %.1f%% done in %.1f sec.' 
+            % (bar, percents, run_time))
+        sys.stdout.flush()
+    return RV
+
+
+def main():
+    import warnings
+    warnings.filterwarnings('error')
+
+    # parse command line options
+    parser = OptionParser()
+    parser.add_option("--anno_file", "-a", dest="anno_file", default=None,
+        help="Annotation file for genes and transcripts in GTF or GFF3")
+    parser.add_option("--sam_file", "-s", dest="sam_file", default=None,
+        help=("Sorted and indexed bam/sam files, use ',' for replicates "
+        "e.g., rep1.sorted.bam,sam1_rep2.sorted.bam"))
+    parser.add_option("--out_dir", "-o", dest="out_dir", default="output", 
+        help="Full path of output directory")
+    parser.add_option("--factor_file", "-f", dest="factor_file", default=None,
+        help=("Features in csv.gz file to predict isoform expression."))
+    # parser.add_option("--gene_file", "-c", dest="gene_file", default=None,
+    #     help=("Gene features, the same order of the input genes."))
+    # parser.add_option("--cell_file", "-c", dest="cell_file", default=None,
+    #     help=("Cell features, the same order of the input sam files."))
+
+    group = OptionGroup(parser, "Optional arguments")
+    group.add_option("--nproc", "-p", type="int", dest="nproc", default="4",
+        help="Number of subprocesses [default: %default]")
+    group.add_option("--weight_file", "-w", dest="weight_file", default=None,
+        help=("File with weights, an output of Brie."))
+    group.add_option("--ftype", "-y", dest="ftype", default="Y",
+        help="Type of function target: FPKM, Y, Psi [default: %default].")
+    
+    group.add_option("--fLen", type="float", nargs=2, dest="frag_leng",
+        default=[None,None], help=("Two arguments for fragment length: "
+        "mean and standard diveation, default: auto-detected"))
+    group.add_option("--bias", nargs=3, dest="bias_args",
+        default=["unif","None","None"], help=("Three argments for bias "
+        "correction: BIAS_MODE,REF_FILE,BIAS_FILE(s). BIAS_MODE: unif, end5, "
+        "end3, both. REF_FILE: the genome reference file in fasta format. "
+        "BIAS_FILE(s): bias files from dice-bias, use '---' for time specific "
+        "files, [default: unif None None]"))
+
+    group.add_option("--sigma", dest="_sigma", default=None,
+        help=("Sigma in Bayesian regression: the Gaussian standard deviation "
+        "of residues [default: Auto]."))
+    group.add_option("--lambda", dest="_lambda", default="0.1",
+        help=("Lambda in Bayesian regression: the coeffiecient of "
+        "L2 constrain on weights [default: %default]."))
+
+    group.add_option("--mcmc", type="int", nargs=4, dest="mcmc_run",
+        default=[500,5000,1000,50], help=("Four arguments for in MCMC "
+        "iterations: save_sample,max_run,min_run,gap_run. Required: "
+        "save_sample =< 3/4*mim_run. [default: 500 5000 1000 50]"))
+
+    # group.add_option("--add_premRNA", action="store_true", dest="add_premRNA", 
+    #     default=False, help="Add the pre-mRNA as a transcript")
+    # parser.add_option("--feature_log",action="store_true",dest="feature_log",
+    #     default=False, help="Use log scale for all features.")
+    # parser.add_option("--two_isoform",action="store_true",dest="two_isoform",
+    #     default=False, help=("Only two isoforms for all genes. This is mainly "
+    #     "for splicing events."))
+
+    parser.add_option_group(group)
+
+    (options, args) = parser.parse_args()
+    if len(sys.argv[1:]) == 0:
+        print("Welcome to Brie!\n")
+        print("use -h or --help for help on argument.")
+        sys.exit(1)
+    if options.anno_file == None:
+        print("[Brie] Error: need --anno_file for annotation.")
+        sys.exit(1)
+    else:
+        sys.stdout.write("\r[Brie] loading annotation file... ")
+        sys.stdout.flush()
+        # anno = load_annotation(options.anno_file, options.anno_source)
+        genes = load_genes(options.anno_file)
+        sys.stdout.write("\r[Brie] loading annotation file... Done.\n")
+        sys.stdout.flush()
+        # genes = anno["genes"]
+        tran_len = []
+        tran_ids = []
+        gene_ids = []
+        for g in genes:
+            for t in g.trans:
+                tran_len.append(t.tranL)
+                tran_ids.append(t.tranID)
+                gene_ids.append(g.geneID)
+        gene_ids = np.array(gene_ids)
+        tran_ids = np.array(tran_ids)
+        tran_len = np.array(tran_len)
+
+        global TOTAL_GENE, TOTAL_TRAN
+        TOTAL_GENE = len(genes)
+        TOTAL_TRAN = len(tran_ids)
+
+    if options.sam_file == None:
+        print("[Brie] Error: need --sam_file for indexed and aliged reads.")
+        sys.exit(1)
+    else:
+        global TOTAL_READ
+        TOTAL_READ = 0
+        sam_file = options.sam_file
+        for ss in sam_file.split(","):
+            if not os.path.isfile(ss):
+                print("Error: No such file\n    -- %s" %ss)
+                sys.exit(1)
+            pysam_stats = pysam.idxstats(ss)
+            if type(pysam_stats) is not list:
+                pysam_stats = pysam_stats.split("\n")
+            for tp in pysam_stats: 
+                tmp = tp.strip().split("\t")
+                if len(tmp) >= 3:
+                    TOTAL_READ += float(tmp[2])
+
+    two_isoform = True
+    if options.factor_file == None:
+        feature_all = np.zeros((len(tran_ids), 1))
+        feature_ids = ["zero"]
+        if two_isoform: 
+            idxF = np.arange(0, len(tran_ids), 2)
+            feature_all[idxF+1,:] = None
+        else:
+            idxF = np.arange(0, len(tran_ids))
+    else:
+        feature_all, feature_ids, idxF = map_data(options.factor_file,
+            tran_ids, False) #options.feature_log
+
+    if options.out_dir is None:
+        out_dir = os.path.dirname(os.path.abspath(ss)) + "/brie_out"
+    else:
+        out_dir = options.out_dir
+    try:
+        os.stat(os.path.abspath(out_dir))
+    except:
+        os.mkdir(os.path.abspath(out_dir))
+
+    if options.weight_file == None:
+        weights_in = None
+    else:
+        weights_in = np.loadtxt(options.weight_file, dtype="str", skiprows=1)
+        weights_in = weights_in[:, 1].astype(float).reshape(-1)
+    if options._sigma is None:
+        _sigma = None
+    else:
+        _sigma = float(options._sigma)
+    if options._lambda is None:
+        _lambda = None
+    else:
+        _lambda = float(options._lambda)
+
+    bias_mode, ref_file, bias_file = options.bias_args
+    if bias_mode == "unif":
+        ref_file = None
+        bias_file = None
+    elif ref_file is "None": 
+        ref_file = None
+        bias_file = None
+        bias_mode = "unif"
+        print("[Brie] No reference sequence, change to uniform mode.")
+    elif bias_file is "None":
+        ref_file = None
+        bias_file = None
+        bias_mode = "unif"
+        print("[Brie] No bias parameter file, change to uniform mode.")
+    else:
+        bias_file = bias_file.split("---")
+
+    no_twice = False
+    auto_min = 200
+    mate_mode = "pair"
+    two_isoform = True
+    add_premRNA = False
+    print_detail = False
+
+    nproc = options.nproc
+    ftype = options.ftype
+    FLmean, FLstd = options.frag_leng
+    sample_num, M, initial, gap = options.mcmc_run
+
+    # print(gene_ids)
+    # import h5py
+    # f = h5py.File(os.path.join(out_dir, "samples.h5"), "w")
+    # # f.create_dataset("gene_ids", data=gene_ids, compression="gzip")
+    # # f.create_dataset("tran_ids", data=tran_ids, compression="gzip")
+    # f.create_dataset("features", data=feature_all, compression="gzip")
+    # f.create_dataset("feature_ids", data=feature_ids, compression="gzip")
+    # # f.create_dataset("W_sample", data=W_all[:,-min(m2,sample_num):],
+    # #     compression="gzip", compression_opts=9)
+    # # f.create_dataset("Psi_sample", data=Psi_all[:,-min(m1,sample_num):],
+    # #     compression="gzip", compression_opts=9)
+    # # f.create_dataset("FPKM", data=RPK_all[:,-m1:].mean(axis=1),
+    # #     compression="gzip", compression_opts=9)
+    # # f.create_dataset("counts", data=Cnt_all[:,-m1:].mean(axis=1),
+    # #     compression="gzip", compression_opts=9)
+    # # f.create_dataset("sigma", data=np.array([sigma_]), compression="gzip")
+    # f.close()
+
+    # exit()
+
+    print("[Brie] loading reads for %d genes with %d cores..." %(TOTAL_GENE, 
+        nproc))
+    global START_TIME
+    START_TIME = time.time()
+
+    R_all, len_iso_all, prob_iso_all = [], [], []
+    if nproc <= 1:
+        for g in genes:
+            RV = set_info(g, sam_file, bias_mode, ref_file, bias_file, FLmean,
+                FLstd, mate_mode, auto_min)
+            show_progress(RV)
+            R_all.append(RV["Rmat"])
+            len_iso_all.append(RV["len_iso"])
+            prob_iso_all.append(RV["prob_iso"])
+
+    else:
+        pool = multiprocessing.Pool(processes=nproc)
+        result = []
+        for g in genes:
+            result.append(pool.apply_async(set_info, (g, sam_file, bias_mode,
+                ref_file, bias_file, FLmean, FLstd, mate_mode, auto_min), 
+                callback=show_progress))
+        pool.close()
+        pool.join()
+        for res in result:
+            RV = res.get()
+            R_all.append(RV["Rmat"])
+            len_iso_all.append(RV["len_iso"])
+            prob_iso_all.append(RV["prob_iso"])
+
+    
+    print("\n[Brie] running Brie for %d isoforms on %d genes with %d cores..." 
+        %(TOTAL_TRAN, TOTAL_GENE, nproc))
+
+    Psi_all, Y_all, RPK_all, Cnt_all, W_all, sigma_ = brie_MH_Heuristic(R_all,
+        len_iso_all, prob_iso_all, feature_all, idxF, weights_in=weights_in, 
+        _sigma=_sigma, _lambda=_lambda, ftype=ftype, total_count=TOTAL_READ, 
+        M=M,  Mmin=initial, gap=gap, nproc=nproc)
+
+    save_data(out_dir, sample_num, gene_ids, tran_ids, tran_len, feature_all,
+        feature_ids, Psi_all, RPK_all, Cnt_all, W_all, sigma_)
+
+
+
+if __name__ == "__main__":
+    main()
+