Merge pull request #36 from yhoogstrate/fuma_compatibility_changes

FuMa compatibility changes
yhoogstrate · Jul 8, 2016 · 5af7958 · 5af7958
2 parents 17a7fb0 + 55769f7
commit 5af7958
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Showing 5 changed files with 19 additions and 6 deletions.
diff --git a/Changelog b/Changelog
@@ -1,3 +1,7 @@
+2016-07-08  Youri Hoogstrate
+
+	* Version 3.0.3: API Changes, only useful for tools depending on FuMa as lib
+
 2016-04-07  Youri Hoogstrate
 
 	* Version 3.0.2: Suppresses a warning that occurs in some installations

diff --git a/fuma/Fusion.py b/fuma/Fusion.py
@@ -21,8 +21,9 @@
  <http://epydoc.sourceforge.net/manual-fields.html#fields-synonyms>
 """
 
-STRAND_FORWARD = True
-STRAND_REVERSE = False
+STRAND_FORWARD      = True
+STRAND_REVERSE      = False
+STRAND_UNDETERMINED = None
 
 # Acceptor-Donor direction equal to lexicographical order?
 AD_DIRECTION_FORWARD = True
@@ -284,7 +285,7 @@ def has_annotated_genes(self):
 		return self.annotated_genes_left and self.annotated_genes_right
 
 	def show_me(self):
-		print self.__str__()
+		print(self.__str__())
 
 	def __str__(self):
 		pos_left = self.get_left_position(True)

diff --git a/fuma/Readers.py b/fuma/Readers.py
@@ -24,8 +24,8 @@
 import logging,sys
 import re
 
-from Fusion import Fusion
-from FusionDetectionExperiment import FusionDetectionExperiment
+from fuma.Fusion import Fusion
+from fuma.FusionDetectionExperiment import FusionDetectionExperiment
 
 class ReadCGhighConfidenceJunctionsBeta(FusionDetectionExperiment):
 	logger = logging.getLogger("FuMa::Readers::ReadCGhighConfidenceJunctionsBeta")

diff --git a/fuma/__init__.py b/fuma/__init__.py
@@ -21,7 +21,7 @@
  <http://epydoc.sourceforge.net/manual-fields.html#fields-synonyms>
 """
 
-__version_info__ = ('3', '0', '2')
+__version_info__ = ('3', '0', '3')
 __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3]
 __author__ = 'Youri Hoogstrate'
 __homepage__ = 'https://github.com/yhoogstrate/fuma'

diff --git a/test_ComparisonTriangle.test_cfbsg_02_b.output.txt b/test_ComparisonTriangle.test_cfbsg_02_b.output.txt
@@ -0,0 +1,8 @@
+Left-genes	Right-genes	Spans large gene (>200000bp)	TestExperimentA	TestExperimentB
+NM_00000C	NM_00000D	FALSE	CLUSTER2=chr3:10000-chr4:20000	
+NM_00000E	NM_00000F	FALSE	CLUSTER3=chr5:10000-chr6:20000	
+NM_00000G	NM_00000H	FALSE	CLUSTER4=chr7:10000-chr8:20000	
+NM_00000C	NM_00000D	FALSE		CLUSTER2=chr3:10000-chr4:20000
+NM_00000E	NM_00000F	FALSE		CLUSTER3=chr5:10000-chr6:20000
+NM_00000G	NM_00000H	FALSE		CLUSTER4=chr7:10000-chr8:20000
+NM_00000A	NM_00000B	FALSE	CLUSTER1=chr1:10000-chr2:20000	CLUSTER1=chr1:10000-chr2:20000