Merge pull request #38 from yhoogstrate/compat2

Pypi compatibility updates

.gitignore

@@ -42,3 +42,6 @@ nosetests.xml
 #/test_*
 #/tests/bak/
 output_fuma.txt
+/htmlcov/*
+.venv
+/*.txt

.travis.yml

@@ -7,9 +7,11 @@ python:
 #  - "3.4"
 #  - "nightly"
 # command to install dependencies
-install: "pip install ."
-# command to run tests
-script: "python setup.py test"
+install:
+  - "virtualenv -p python2 .venv ; source .venv/bin/activate ; apt-get install python-numpy ; pip install HTSeq ; python setup.py install"
+
+script:
+  - "source .venv/bin/activate ; nosetests -v tests/*.py"
 
 notifications:
   email: false

Changelog

@@ -1,3 +1,11 @@
+2016-07-11  Youri Hoogstrate
+
+	* Version 3.0.5: Changes in deployment & two fixes in export function
+
+2016-07-11  Youri Hoogstrate
+
+	* Version 3.0.4: Changes in deployment
+
 2016-07-08  Youri Hoogstrate
 
 	* Version 3.0.3: API Changes, only useful for tools depending on FuMa as lib

MANIFEST.in

@@ -0,0 +1,4 @@
+include fuma
+include bin
+include test
+reverse-exclude Distutils*

README.md

@@ -39,7 +39,7 @@ Bioinformatics first published online December 10, 2015
 - [References](#references)
 
 ## Introduction ##
-This is the Manual as part of the Supplementary Material that belongs to the manuscript: *FuMa: reporting overlap in RNA-seq detected fusion genes* (under submission). FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location and corresponding annotated genes. It is the organisation of the transcriptome (provided by the user) that forms the basis for FuMa to consider fusion genes to be identical or not. The provided gene annotation can be adjusted to define the biological question. For example, if it is desired to only consider fusion events that occur within exons, FuMa can be provided a list of such regions instead of entire genes. Currently FuMa supports input files from:
+This is the Manual as part of the Supplementary Material that belongs to the manuscript: *FuMa: reporting overlap in RNA-seq detected fusion genes*. FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location and corresponding annotated genes. It is the organisation of the transcriptome (provided by the user) that forms the basis for FuMa to consider fusion genes to be identical or not. The provided gene annotation can be adjusted to define the biological question. For example, if it is desired to only consider fusion events that occur within exons, FuMa can be provided a list of such regions instead of entire genes. Currently FuMa supports input files from:
 
 +	Chimera (Beccuti et al., 2014)
 +	ChimeraScan (Iyer et al., 2011)

coverage.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+py.test --cov-report html --cov=fuma tests

deploy.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+#pandoc --reference-links --no-wrap -t rst "README.md" > "README.rst"
+#python2 setup.py --long-description | rst2html.py > build/README.html
+python2 setup.py sdist upload

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:

fuma/GeneAnnotation.py

@@ -21,6 +21,7 @@
  <http://epydoc.sourceforge.net/manual-fields.html#fields-synonyms>
 """
 
+#import gffutils
 import HTSeq
 import logging
 
@@ -33,6 +34,9 @@ class GeneAnnotation:
 	def __init__(self,name):
 		self.n = 0
 		self.name = name
+
+		# list(db.region(region=('2L', 9277, 10000), completely_within=True))
+		#self.gas2 = gffutils.create_db(gtf, dbfn=db_file)
 		self.gas = HTSeq.GenomicArrayOfSets("auto", stranded=False)
 
 	def add_annotation(self,gene,chromosome,start,stop):
@@ -63,5 +67,5 @@ def __iter__(self):
 			for gene in list(reduce(lambda s1, s2: s1 | s2, [x[1] for x in self.gas[HTSeq.GenomicInterval(chromosome_name,0,chromosome_obj['.'].iv.end)].steps()])):
 				yield gene
 
-	def show_me(self):
-		print self.__str__()
+	#def show_me(self):
+	#	print self.__str__()

fuma/OverlapComplex.py

@@ -44,18 +44,18 @@ def add_experiment(self,experiment):
 		self.dataset_names.append(experiment.name)
 		self.matches_total[str(len(self.datasets))] = len(experiment)
 
-	def create_matrix(self,n):
-		matrix = []
-		for dataset in self.datasets:
-			matrix.append([])
-
-		n = len(self.datasets)-1
-		while(n >= 1):
-			for i in range(n):
-				matrix[n].append(i)
-			n -= 1
-
-		return matrix
+	#def create_matrix(self,n):
+	#	matrix = []
+	#	for dataset in self.datasets:
+	#		matrix.append([])
+	#	
+	#	n = len(self.datasets)-1
+	#	while(n >= 1):
+	#		for i in range(n):
+	#			matrix[n].append(i)
+	#		n -= 1
+	#	
+	#	return matrix
 
 	def create_keys(self,combination):
 		keys = [combination[:-1],combination[-1:],combination]

fuma/__init__.py

@@ -21,8 +21,9 @@
  <http://epydoc.sourceforge.net/manual-fields.html#fields-synonyms>
 """
 
-__version_info__ = ('3', '0', '3')
+__version_info__ = ('3', '0', '5')
 __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3]
 __author__ = 'Youri Hoogstrate'
+__author_email__ = '_@.'
 __homepage__ = 'https://github.com/yhoogstrate/fuma'
 __license__ = 'GNU General Public License v3 (GPLv3)'

setup.py

@@ -23,20 +23,23 @@
 
 import fuma
 
-from distutils.core import setup
-from setuptools import setup, find_packages
+from setuptools import setup
 
 setup(name='fuma',
 		version=fuma.__version__,
 		description='Fusion Matcher',
+		long_description="FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location and corresponding annotated genes. It is the organisation of the transcriptome (provided by the user) that forms the basis for FuMa to consider fusion genes to be identical or not. The provided gene annotation can be adjusted to define the biological question. For example, if it is desired to only consider fusion events that occur within exons, FuMa can be provided a list of such regions instead of entire genes.",
 		author=fuma.__author__,
+		author_email=fuma.__author_email__,
 		maintainer=fuma.__author__,
 		license=fuma.__license__,
 		url=fuma.__homepage__,
 		scripts=["bin/fuma","bin/defuse-clusters-to-CG",'bin/chimerascan-exclude-transcriptome-events',"bin/fusioncatcher-to-CG","bin/chimerascan-relative-bedpe-to-CG","bin/fuma-list-to-boolean-list","bin/fuma-gencode-gtf-to-bed"],
 		packages=['fuma'],
 		test_suite="tests",
-		install_requires=['HTSeq >= 0.6.1','numpy'],
+		platforms=['any'],
+		setup_requires=['numpy'],
+		install_requires=['numpy','HTSeq >= 0.6.1','nose'],
 		classifiers=[
 			'Environment :: Console',
 			'Intended Audience :: Science/Research',