diff --git a/Changelog b/Changelog index 19daa5c..83c7709 100644 --- 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 index 284a6de..a6d112c 100644 --- a/fuma/Fusion.py +++ b/fuma/Fusion.py @@ -21,8 +21,9 @@ """ -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 index 75849a4..d89be21 100644 --- 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 index c11b14d..e21c0cb 100644 --- a/fuma/__init__.py +++ b/fuma/__init__.py @@ -21,7 +21,7 @@ """ -__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 new file mode 100644 index 0000000..0a595ac --- /dev/null +++ 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