Add acidbio/bed tests

.github/workflows/main.yml

@@ -46,5 +46,13 @@ jobs:
       - name: Run tests
         run: pytest --cov=./ --cov-report=xml
 
+      - name: Run acidbio BED tests
+        run: |
+          git clone https://github.com/mdshw5/acidbio.git
+          cd acidbio/bed
+          python3 -m pip install -r requirements.txt
+          cp config_template.yaml config.yaml
+          python3 bedrunall.py --tool pyfaidx BED03 ./
+
       - name: Codecov
         uses: codecov/[email protected]

dev-requirements.txt

@@ -8,6 +8,6 @@ pysam
 requests 
 coverage 
 pyfasta 
-pyvcf 
+pyvcf3
 numpy 
 biopython

pyfaidx/__init__.py

@@ -1117,7 +1117,7 @@ def __init__(self,
         try:
             import vcf
         except ImportError:
-            raise ImportError("PyVCF must be installed for FastaVariant.")
+            raise ImportError("PyVCF3 must be installed for FastaVariant.")
         if call_filter is not None:
             try:
                 key, expr, value = call_filter.split()  # 'GQ > 30'
@@ -1245,6 +1245,8 @@ def map_to_function(rname):
 
 
 def bed_split(bed_entry):
+    if bed_entry[0] == "#":
+        return (None, None, None)
     try:
         rname, start, end = bed_entry.rstrip().split()[:3]
     except (IndexError, ValueError):

pyfaidx/cli.py

@@ -25,6 +25,9 @@ def write_sequence(args):
     header = False
     for region in regions_to_fetch:
         name, start, end = split_function(region)
+        # allow the split_funtion to return None to signify input we should skip
+        if name == None:
+            continue
         if args.size_range:
             if start is not None and end is not None:
                 sequence_len = end - start