Hotfix/issue4 empty ambig bookkeeping (#5)

* addressing issue #4
* added check for empty ambig_dumpfile
* version -> 1.0.1
minors:
* removed pyyaml requirement
* import version from gffquant module

Author: cschu

gffquant/__init__.py

@@ -1 +1 @@
-__version__ = "1.0"
+__version__ = "1.0.1"

gffquant/feature_quantifier.py

@@ -275,18 +275,25 @@ def process_data(self, bamfile):
 		self.gff_dbm.clear_caches()
 
 		# second pass: process ambiguous alignment groups
-		if self.require_ambig_bookkeeping():
-			t0 = time.time()
-
-			ambig_aln = self._read_ambiguous_alignments(ambig_dumpfile)
-			n_align = self._process_ambiguous_aln_groups(ambig_aln)
+		if ambig_dumpfile:
+			if os.path.isfile(ambig_dumpfile) and os.stat(ambig_dumpfile).st_size > 0:
+				t0 = time.time()
 
-			if not DEBUG:
-				os.remove(ambig_dumpfile)
+				ambig_aln = self._read_ambiguous_alignments(ambig_dumpfile)
+				n_align = self._process_ambiguous_aln_groups(ambig_aln)
 
-			t1 = time.time()
-			print("Processed {n_align} secondary alignments in {n_seconds:.3f}s.".format(
-				n_align=n_align, n_seconds=t1-t0), flush=True)
+				t1 = time.time()
+				print("Processed {n_align} secondary alignments in {n_seconds:.3f}s.".format(
+					n_align=n_align, n_seconds=t1-t0), flush=True)
+			else:
+				print("Warning: ambig-mode chosen, but bamfile does not contain secondary alignments.")
+				self.overlap_counter.has_ambig_counts = True # we expect ambig cols in the outfile!
+
+			try:
+				if not DEBUG:
+					os.remove(ambig_dumpfile)
+			except:
+				pass
 
 		self.overlap_counter.annotate_counts(self.bamfile)
 		self.overlap_counter.unannotated_reads += unannotated_ambig

setup.py

@@ -8,14 +8,14 @@
 import re
 import sys
 
-
+from gffquant import __version__ as gffquant_version
 here = path.abspath(path.dirname("__file__"))
 
 with open(path.join(here, "DESCRIPTION.md"), encoding="utf-8") as description:
 	description = long_description = description.read()
 
 	name="gffquant"
-	version = [line.strip().split(" ")[-1] for line in open("gffquant/__init__.py") if line.startswith("__version__")][0]
+	version = gffquant_version
 
 	if sys.version_info.major != 3:
 		raise EnvironmentError("""{toolname} is a python module that requires python3, and is not compatible with python2.""".format(toolname=name))
@@ -33,7 +33,7 @@
 			"Development Status :: 4 - Beta",
 			"Topic :: Scientific Engineering :: Bio/Informatics",
 			"License :: OSI Approved :: MIT License",
-	        "Operating System :: POSIX :: Linux",
+			"Operating System :: POSIX :: Linux",
 			"Programming Language :: Python :: 3.7"
 		],
 		zip_safe=False,