Merge pull request #40 from COMBINE-lab/develop

fix: fix bug in format detection for id-to-name

.github/workflows/testing.yml

@@ -15,9 +15,9 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda install -n base python=3.9 conda-forge::biopython bioconda::pyranges packaging bioconda::scanpy pytest -y
+        conda install -n base python=3.9 conda-forge::biopython numpy==1.23 bioconda::pyranges==0.0.120 packaging bioconda::scanpy pytest -y
 
     - name: pytest
       run: |
         pip install .
-        pytest
+        pytest

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyroe
-version = 0.9.2
+version = 0.9.3
 author = Dongze He, Rob Patro
 author_email = [email protected], [email protected]
 description = utilities of alevin-fry

src/pyroe/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 
 from pyroe.load_fry import load_fry
 from pyroe.make_txome import make_splici_txome, make_spliceu_txome

src/pyroe/id_to_name.py

@@ -6,31 +6,35 @@
 
 def id_to_name(params):
     format_map = {
-        ".gtf": pyranges.read_gtf,
-        ".gff": pyranges.read_gff3,
-        ".gff3": pyranges.read_gff3,
+        "gtf": pyranges.read_gtf,
+        "gff": pyranges.read_gff3,
+        "gff3": pyranges.read_gff3,
     }
     annot_reader = None
     if params.format is None:
         p = pathlib.Path(params.gtf_file)
-        suffs = [z.lower() for z in p.suffixes]
+        suffs = [z.lower().strip('.') for z in p.suffixes]
 
         z = None
-        if len(suffs) == 1:
-            z = suffs[0]
-        elif len(suffs) == 2 and suffs[-1] == ".gz":
-            z = suffs[-2]
+        if len(suffs) >= 1:
+            # look at the final suffix
+            z = suffs[-1]
+            # if the final suffix is gz and there are
+            # suffixes preceding it, check the penultimate
+            # one and use that
+            if z == "gz" and len(suffs) > 1:
+                z = suffs[-2]
 
-        if z in format_map.keys():
-            annot_reader = format_map[z]
-        else:
+        if z is None or z not in format_map.keys():
             logging.error(
                 "Could not determine format of annotation file. Please provide it explicitly."
             )
             sys.exit(1)
+        else:
+            annot_reader = format_map[z]
     else:
         fmt = params.format.lower()
-        if fmt not in ["gtf", "gff3"]:
+        if fmt not in format_map.keys():
             logging.error(
                 f'Format must be either "gtf" or "gff3", but {fmt} was provided.'
             )