revert wrongheaded partial sequence handling

fsac/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.2.1'

fsac/main.py

@@ -2,6 +2,7 @@
 import sys
 from pathlib import Path
 
+from . import __version__
 from .allele_call import allele_call
 from .update import update_directory
 from .tabulate import tabulate_calls
@@ -11,6 +12,10 @@ def arguments():
 
     parser = argparse.ArgumentParser()
 
+    parser.add_argument('-v', '--version',
+                        action='store_true',
+                        help='Print version and exit')
+
     parser.set_defaults(func=None)
     subparsers = parser.add_subparsers(title='Commands')
 
@@ -76,6 +81,10 @@ def arguments():
 
     args = parser.parse_args()
 
+    if args.version:
+        print('fsac', __version__)
+        sys.exit(0)
+
     if args.func is None:
         parser.print_help()
         sys.exit(0)

fsac/tabulate.py

@@ -42,7 +42,7 @@ def parse_gene_calls_from_json(jsonfile: Path):
 
                 call = '-1'
 
-            elif locus_data['Partial']:
+            elif locus_data['PercentLength'] < 1:
 
                 call = '-2'
 

fsac/update.py

@@ -34,7 +34,7 @@ def update_locus(gene: Dict[str, Union[str, int, bool, float]],
 
     # Non-contig trucation
     if gene['PercentLength'] < 1:
-        return gene['SubjAln'], None
+        return None , None
 
     seq = gene['SubjAln'].replace('-', '')
 
@@ -65,12 +65,6 @@ def update_genome(genome_data: Dict[str, GeneData], genes_dir: Path):
         if seq is None and name is None:
             continue
 
-        # If there is a non-contig truncation
-        if seq is not None and name is None:
-
-            gene['Partial'] = True
-            continue
-
         # TODO ensure null matches are handled appropriately
         gene['Mismatches'] = 0
         gene['Gaps'] = 0

setup.py

@@ -1,9 +1,10 @@
+from fsac import __version__
 from setuptools import setup, find_packages
 
 setup(
 
     name='fsac',
-    version='0.1',
+    version=__version__,
     packages=find_packages(),
     install_requires=[
         'pandas>=0.22.0'