Cn bugfix (#95)

bug fix when parsing clonal string

Author: vineetbansal

setup.py

@@ -76,7 +76,7 @@ def build_extension(self, ext):
 
 setup(
     name='hatchet',
-    version='0.4.5',
+    version='0.4.6',
     packages=['hatchet', 'hatchet.utils', 'hatchet.utils.solve', 'hatchet.bin', 'hatchet.data'],
     package_dir={'': 'src'},
     package_data={'hatchet': ['hatchet.ini'], 'hatchet.data': ['*']},

src/hatchet/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.4.5'
+__version__ = '0.4.6'
 
 import os.path
 from importlib.resources import path

src/hatchet/utils/ArgParsing.py

@@ -228,7 +228,7 @@ def parse_count_reads_arguments(args=None):
     if not os.path.isfile(normalbaf): raise ValueError(sp.error("The specified normal BAM file does not exist"))
     tumors = args.tumors
     for tumor in tumors:
-        if(not os.path.isfile(tumor)): raise ValueError(sp.error("The specified normal BAM file does not exist"))
+        if(not os.path.isfile(tumor)): raise ValueError(sp.error(f"The specified tumor BAM file {tumor} does not exist"))
     names = args.samples
     if names != None and (len(tumors)+1) != len(names):
         raise ValueError(sp.error("A sample name must be provided for each corresponding BAM: both for each normal sample and each tumor sample"))

src/hatchet/utils/solve/utils.py

@@ -33,16 +33,19 @@ def parse_clonal(clonal):
     copy_numbers = OrderedDict()  # dict from cluster_id => (cn_a, cn_b) 2-tuple
     clonal_parts = clonal.split(',')
     n_clonal_parts = len(clonal_parts)
-    cn_totals = set()
 
-    for c in clonal_parts:
+    for i, c in enumerate(clonal_parts):
         cluster_id, cn_a, cn_b = [int(_c) for _c in c.split(':')]
+
+        # The first two clonal clusters (used for scaling) MUST have different total copy numbers
+        if i==1:
+            _first_cn_a, _first_cn_b = list(copy_numbers.values())[0]
+            if _first_cn_a + _first_cn_b == cn_a + cn_b:
+                raise ValueError('When >= 2 clonal copy numbers are given, the first two must be different in the two segmental clusters')
+
         cn_total = cn_a + cn_b
         if (cn_total == 2) and (n_clonal_parts > 1):
             warnings.warn('Please specify a single cluster when CN_A+CN_B=2')
-        if cn_total in cn_totals:
-            raise ValueError('Cannot specify two clusters with same CN_A+CN_B')
-        cn_totals.add(cn_total)
         if cluster_id in copy_numbers:
             raise ValueError('Already encountered cluster_id =', str(cluster_id))
         copy_numbers[cluster_id] = cn_a, cn_b