brie 2.2.3__tar.gz → 2.3.1__tar.gz

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

@@ -0,0 +1,27 @@
+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/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "brie-tutorials"]
+	path = brie-tutorials
+	url = https://github.com/huangyh09/brie-tutorials

brie-2.3.1/.readthedocs.yml

@@ -0,0 +1,32 @@
+# .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/MANIFEST.in

@@ -0,0 +1,2 @@
+include requirements.txt
+include README.rst

{brie-2.2.3 → brie-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: brie
-Version: 2.2.3
+Version: 2.3.1
 Summary: BRIE: Bayesian regression for isoform estimate
 Home-page: https://brie.readthedocs.io
 Author: Yuanhua Huang

{brie-2.2.3 → brie-2.3.1}/brie/bin/count.py

@@ -17,7 +17,7 @@ from ..utils.io_utils import read_brieMM, read_gff, convert_to_annData
 #TODO: something wrong as there is no reads for isoform 2. Please check!!
 
 def smartseq_count(gff_file, samList_file, out_dir=None, nproc=1, 
-        event_type='SE', verbose=False):
+        event_type='SE', verbose=False, edge_hang=10, junc_hang=2):
     """CLI for counting reads supporting isoforms
     """
     # Parameter check
@@ -102,7 +102,7 @@ def smartseq_count(gff_file, samList_file, out_dir=None, nproc=1,
           %(len(genes), sam_table.shape[0], nproc))
 
     get_smartseq_matrix(genes, sam_table, out_dir, event_type=event_type, 
-        edge_hang=10, junc_hang=2, nproc=nproc, verbose=verbose)
+        edge_hang=edge_hang, junc_hang=junc_hang, nproc=nproc, verbose=verbose)
     
 
     ## Don't save into h5ad if not all genes only with two isoforms
@@ -134,7 +134,8 @@ def smartseq_count(gff_file, samList_file, out_dir=None, nproc=1,
 
 
 def droplet_count(gff_file, sam_file, barcode_file, out_dir=None, nproc=1, 
-                  event_type='SE', CB_tag='CB', UMI_tag='UR', verbose=False):
+                  event_type='SE', CB_tag='CB', UMI_tag='UR', verbose=False,
+                  edge_hang=10, junc_hang=2):
     """CLI for counting reads supporting isoforms
     """
     ## TODO: Parameter check
@@ -217,7 +218,8 @@ def droplet_count(gff_file, sam_file, barcode_file, out_dir=None, nproc=1,
           %(len(genes), cell_list.shape[0], nproc))
 
     res = get_droplet_matrix(genes, sam_file, cell_list, out_dir, event_type, 
-                             10, 2, CB_tag, UMI_tag, nproc, verbose)
+                             edge_hang, junc_hang, CB_tag, UMI_tag, nproc, 
+                             verbose)
     
     ## Don't save into h5ad if not all genes only with two isoforms
     n_trans = [len(g.trans) for g in genes]
@@ -278,6 +280,13 @@ def main():
     group2.add_option("--eventType", "-t", dest="event_type", default="SE",
         help="Type of splicing event for check. SE: skipping-exon; "
              "Any: no-checking [default: %default]")
+
+    group3 = OptionGroup(parser, "Reads compatibility")
+    group3.add_option("--minMatch", type="int", dest="min_match", default="10", 
+        help="Min matched bases to the isoform; consider the read length and "
+             "transcript completeness [default: %default]")
+    group3.add_option("--maxMiss", type="int", dest="max_miss", default="2", 
+        help="Max missed bases in the isoform range [default: %default]")
     
     # group.add_option("--add_premRNA", action="store_true", dest="add_premRNA", 
     #     default=False, help="Add the pre-mRNA as a transcript")
@@ -285,6 +294,7 @@ def main():
     parser.add_option_group(group0)
     parser.add_option_group(group1)
     parser.add_option_group(group2)
+    parser.add_option_group(group3)
     
     (options, args) = parser.parse_args()
     if len(sys.argv[1:]) == 0:
@@ -301,11 +311,13 @@ def main():
     
     if options.samList_file is not None:
         smartseq_count(options.gff_file, options.samList_file, options.out_dir, 
-            options.nproc, options.event_type, options.verbose)
+            options.nproc, options.event_type, options.verbose, 
+            options.min_match, options.max_miss)
     else:
         droplet_count(options.gff_file, options.sam_file, options.barcodes_file, 
-            options.out_dir, options.nproc, options.event_type, options.cell_tag,
-            options.UMI_tag, options.verbose)
+            options.out_dir, options.nproc, options.event_type, 
+            options.cell_tag, options.UMI_tag, options.verbose, 
+            options.min_match, options.max_miss)
 
 
 if __name__ == "__main__":

{brie-2.2.3 → brie-2.3.1}/brie/utils/count.py

@@ -118,26 +118,34 @@ def _get_segment(exons, read):
 def check_reads_compatible(transcript, reads, edge_hang=10, junc_hang=2):
     """Check if reads are compatible with a transcript
     """
+    # TODO: the configuration can be further optimized
+    max_all_miss   = junc_hang
+    max_exon_miss  = junc_hang
+    min_all_match  = edge_hang
+    min_side_match = junc_hang
+
     is_compatible = [True] * len(reads)
     for i in range(len(reads)):
         _segs = _get_segment(transcript.exons, reads[i])
         
         # check mismatch to regions not in this transcript
-        if len(reads[i].positions) - sum(_segs) >= junc_hang:
+        if len(reads[i].positions) - sum(_segs) >= max_all_miss:
             is_compatible[i] = False
             continue
 
         # check if edge hang is too short
-        if (_segs[0] > 0 or _segs[-1] > 0) and sum(_segs[1:-1]) < edge_hang:
+        # it may be determined by reads length and transcript completeness
+        if (_segs[0] > 0 or _segs[-1] > 0) and sum(_segs[1:-1]) < min_all_match:
             is_compatible[i] = False
             continue
             
         # check if exon has been skipped
-        if len(_segs) > 4:
+        if len(_segs) > 2:
             for j in range(2, len(_segs) - 2):
-                if (_segs[j-1] >= junc_hang and _segs[j+1] >= junc_hang and
-                    transcript.exons[j-1, 1] - transcript.exons[j-1, 0] - 
-                    _segs[j] >= junc_hang):
+                exon_len = transcript.exons[j-1, 1] - transcript.exons[j-1, 0]
+                if (_segs[j-1] >= min_side_match and 
+                    _segs[j+1] >= min_side_match and
+                    (exon_len - _segs[j]) >= max_exon_miss):
                     is_compatible[i] = False
                     break
 
@@ -180,12 +188,16 @@ def fetch_reads_count(gene, sam_file, event_type="SE", RNA_type="spliced",
         idx_U1 = np.arange(n_readsPE, n_readsPE + n_readsU1)
         idx_U2 = np.arange(n_readsPE + n_readsU1, n_reads)
         
-        Rmat[idx_PE, i] = check_reads_compatible(_tran, reads["reads1"])
+        Rmat[idx_PE, i] = check_reads_compatible(
+            _tran, reads["reads1"], edge_hang=edge_hang, junc_hang=junc_hang)
         if len(reads["reads2"]) > 0:
-            Rmat[idx_PE, i] *= check_reads_compatible(_tran, reads["reads2"])
+            Rmat[idx_PE, i] *= check_reads_compatible(
+                _tran, reads["reads2"], edge_hang=edge_hang, junc_hang=junc_hang)
             
-        Rmat[idx_U1, i] = check_reads_compatible(_tran, reads["reads1u"])
-        Rmat[idx_U2, i] = check_reads_compatible(_tran, reads["reads2u"])
+        Rmat[idx_U1, i] = check_reads_compatible(
+            _tran, reads["reads1u"], edge_hang=edge_hang, junc_hang=junc_hang)
+        Rmat[idx_U2, i] = check_reads_compatible(
+            _tran, reads["reads2u"], edge_hang=edge_hang, junc_hang=junc_hang)
     
     return Rmat
 

{brie-2.2.3 → brie-2.3.1}/brie/utils/io_utils.py

@@ -48,8 +48,7 @@ def convert_to_annData(Rmat_dict, effLen_tensor, cell_note, gene_note,
                                effLen_tensor[:, 1, :], axis=1)
     varm['p_ambiguous'] = Prob_tensor[:, :, 2]
     
-    adata = anndata.AnnData(X=X, obs=obs, var=var, varm=varm,
-                            layers=layers, dtype='float32')
+    adata = anndata.AnnData(X=X, obs=obs, var=var, varm=varm, layers=layers)
     return adata
 
 

brie-2.3.1/brie/version.py

@@ -0,0 +1,2 @@
+__version__ = "2.3.1"
+

{brie-2.2.3 → brie-2.3.1}/brie.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: brie
-Version: 2.2.3
+Version: 2.3.1
 Summary: BRIE: Bayesian regression for isoform estimate
 Home-page: https://brie.readthedocs.io
 Author: Yuanhua Huang

{brie-2.2.3 → brie-2.3.1}/brie.egg-info/SOURCES.txt

@@ -1,10 +1,13 @@
 .gitignore
+.gitmodules
 .readthedocs.yml
 .travis.yml
 LICENSE
+MANIFEST.in
 README.rst
 requirements.txt
 setup.py
+.github/workflows/publish.yml
 brie/__init__.py
 brie/settings.py
 brie/version.py

{brie-2.2.3 → brie-2.3.1}/doc/release.rst

@@ -5,7 +5,15 @@ Release notes
 Release in future
 =================
 
-Release v2.2.3 (15/05/2022)
+Release v2.3.1 (03/11/2026)
+===========================
+* fix pypi release by adding requirements.txt
+
+Release v2.3.0 (17/06/2024)
+===========================
+* support arguments: min_match and max_miss
+
+Release v2.2.3 (15/05/2024)
 ===========================
 * minor fix in plotting function brie.pl.count()
 * add submodule brie-tutorials

brie-2.2.3/.readthedocs.yml

@@ -1,16 +0,0 @@
-sphinx:
-  configuration: doc/conf.py
-build:
-  image: latest
-python:
-  version: 3.7
-  install:
-    - requirements: doc/requirements.txt
-    - requirements: requirements.txt
-    - method: pip
-      path: .
-      extra_requirements:
-          - docs
-    - method: setuptools
-      path: package
-  system_packages: true

brie-2.2.3/brie/version.py

@@ -1,2 +0,0 @@
-__version__ = "2.2.3"
-