Travis & small fixes

Author: yhoogstrate

.travis.yml

@@ -8,12 +8,10 @@ python:
 #  - "nightly"
 # command to install dependencies
 install:
-  - sudo apt-get install python-numpy
-  - sudo pip install HTSeq
-  - sudo python setup.py install
+  - "virtualenv -p python2 .venv ; source .venv/bin/activate ; apt-get install python-numpy ; pip install HTSeq ; python setup.py install"
 
 script:
-  - nosetests -v tests/*.py
+  - "source .venv/bin/activate ; nosetests -v tests/*.py"
 
 notifications:
   email: false

Changelog

@@ -1,6 +1,6 @@
 2016-07-11  Youri Hoogstrate
 
-	* Version 3.0.5: Changes in deployment
+	* Version 3.0.5: Changes in deployment & two fixes in export function
 
 2016-07-11  Youri Hoogstrate
 

fuma/ComparisonTriangle.py

@@ -154,7 +154,7 @@ def log_progress(self,n_total, passed, previous_percentage):
 		return n_total, passed, previous_percentage
 
 	def export_list_fg(self,fusion,fh):
-		if(self.args.acceptor_donor_order_specific_matching and fusion.acceptor_donor_direction() == AD_DIRECTION_REVERSE):
+		if(self.args.acceptor_donor_order_specific_matching and fusion.acceptor_donor_direction == AD_DIRECTION_REVERSE):
 			## A-B should be reported as B-A; chr1:123\tchr1:456 as chr1:456-chr1:123
 			fh.write(":".join(sorted(list(set([str(gene) for gene in fusion.get_annotated_genes_right2()])))) + "\t")
 			fh.write(":".join(sorted(list(set([str(gene) for gene in fusion.get_annotated_genes_left2()])))))
@@ -170,7 +170,7 @@ def export_list_fg(self,fusion,fh):
 
 				for location in fusion.locations():
 					if location['dataset'] == dataset.name:
-						strdata.append(str(loc['id'])+"=chr"+loc['right'][0]+':'+str(loc['right'][1])+'-chr'+loc['left'][0]+':'+str(loc['left'][1]))
+						strdata.append(str(location['id'])+"=chr"+location['right'][0]+':'+str(location['right'][1])+'-chr'+location['left'][0]+':'+str(location['left'][1]))
 
 				fh.write(",".join(sorted(strdata)))
 		else: