adding test data to unit test build procedure

proost · Nov 30, 2016 · 47abaf0 · 47abaf0
1 parent b171575
commit 47abaf0
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Showing 13 changed files with 358 additions and 3 deletions.
diff --git a/run_unittest.py b/run_unittest.py
@@ -1,14 +1,15 @@
 #!/usr/bin/env python3
 from coverage import coverage
 
-cov = coverage(branch=True, omit=['virtualenv/*', 'tests/*'])
+cov = coverage(branch=True, omit=['virtualenv/*', 'tests/*', 'config.py'])
 cov.start()
 
 import unittest
 import os
 
-from tests.website import WebsiteTest
-from tests.utils import UtilsTest
+# from tests.website import WebsiteTest
+# from tests.utils import UtilsTest
+from tests.build import BuildTest
 
 if __name__ == '__main__':
     try:

diff --git a/tests/build.py b/tests/build.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+from planet import create_app, db
+
+from flask_testing import TestCase
+
+
+class BuildTest(TestCase):
+    """
+    TestCase to check if the website is functional
+        * a DB will be created and filled with dummy data
+        * an app will be spawned with the testing config, DO NOT run this against a database that is in use !!
+        * the DB will be cleared !
+    """
+
+    def create_app(self):
+        """
+        Creates the app using the tests config (tests/config.py)
+
+        :return: flask app with settings from tests/config.py
+        """
+        app = create_app('tests.config')
+        return app
+
+    def setUp(self):
+        """
+        Creates a database and fills it with sufficient dummy data to run the tests.
+        """
+        db.create_all()
+
+    def tearDown(self):
+        """
+        Removes test database again, so the next test can start with a clean slate
+        """
+        db.session.remove()
+        db.drop_all()
+
+    def test_build(self):
+        from planet.models.species import Species
+        from planet.models.sequences import Sequence
+
+        from planet.models.xrefs import XRef
+        from planet.models.go import GO
+
+        Species.add('mmu', 'Marek mutwiliana')
+        s = Species.query.first()
+
+        Sequence.add_from_fasta('./tests/data/mamut.cds.fasta', s.id)
+        XRef.add_xref_genes_from_file(s.id, './tests/data/mamut.xref.txt')
+        GO.add_from_obo('./tests/data/test_go.obo')
+        GO.add_go_from_tab('./tests/data/functional_data/mamut.go.txt', s.id, source="Fake UnitTest Data")
+
+        test_sequences = Sequence.query.all()
+        test_sequence = Sequence.query.filter_by(name='Gene01').first()
+        test_xref = test_sequence.xrefs[0]
+        test_go = test_sequence.go_labels.first()
+        test_go_association = test_sequence.go_associations.filter_by(evidence=None).first()
+
+        self.assertTrue(len(test_sequences) == 3)                       # Check if all genes are added
+
+        self.assertTrue(test_sequence.aliases == 'BRCA2')               # Check if alias is added and correct
+        self.assertTrue('www.ensembl.org' in test_xref.url)             # Check if url is added
+
+        self.assertTrue(test_go.label == 'GO:0000003')                  # Check if go is added
+        self.assertTrue(test_go_association.go.label == 'GO:0000001')   # Check if go parent is added
diff --git a/tests/data/expression/mamut.expression_annotation.txt b/tests/data/expression/mamut.expression_annotation.txt
@@ -0,0 +1,10 @@
+SampleID	ConditionDescription
+A	Tissue 01
+B	Tissue 01
+C	Tissue 01
+D	Tissue 02
+E	Tissue 02
+F	Tissue 02
+G	Tissue 03
+H	Tissue 03
+I	Tissue 03
diff --git a/tests/data/expression/mamut.expression_order_color.txt b/tests/data/expression/mamut.expression_order_color.txt
@@ -0,0 +1,3 @@
+Tissue 01	rgba(225, 158, 54, 0.5)
+Tissue 02	rgba(104, 29, 255, 0.5)
+Tissue 03	rgba(2, 204, 34, 0.5)
diff --git a/tests/data/expression/mamut.mcl_clusters.txt b/tests/data/expression/mamut.mcl_clusters.txt
@@ -0,0 +1 @@
+Gene01	Gene02
diff --git a/tests/data/expression/mamut.pcc.txt b/tests/data/expression/mamut.pcc.txt
@@ -0,0 +1,2 @@
+Gene01: Gene02(0.71)
+Gene02: Gene01(0.71)
diff --git a/tests/data/expression/mamut.tmp.matrix.txt b/tests/data/expression/mamut.tmp.matrix.txt
@@ -0,0 +1,4 @@
+gene	A.htseq	B.htseq	C.htseq	D.htseq	E.htseq	F.htseq	G.htseq	H.htseq	I.htseq
+Gene01	5.065123	4.394866	5.163173	6.5252372	2.8849534	4.7091107	5.573157	4.718033	5.799339
+Gene02	5.120176	7.337115	3.370472	6.9694873	7.2767113	8.9042121	7.954998	7.470095	8.745305
+Gene03	2.081211	1.125116	1.287691	0.8902363	0.1989783	0.9289251	20.034411	20.334816	21.149522
diff --git a/tests/data/functional_data/mamut.go.txt b/tests/data/functional_data/mamut.go.txt
@@ -0,0 +1,3 @@
+Gene01	GO:0000003	ISS
+Gene01	GO:0000002	ISS
+Gene02	GO:0000003	IEA
diff --git a/tests/data/mamut.cds.fasta b/tests/data/mamut.cds.fasta
@@ -0,0 +1,206 @@
+>Gene01
+ATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAAC
+AAAGCAGATTTAGGACCAATAAGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCA
+CCCTATAATTCTGAACCTGCAGAAGAATCTGAACATAAAAACAACAATTACGAACCAAAC
+CTATTTAAAACTCCACAAAGGAAACCATCTTATAATCAGCTGGCTTCAACTCCAATAATA
+TTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTCCTGTAAAAGAATTAGATAAA
+TTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAGTCTTCGCACAGTG
+AAAACTAAAATGGATCAAGCAGATGATGTTTCCTGTCCACTTCTAAATTCTTGTCTTAGT
+GAAAGTCCTGTTGTTCTACAATGTACACATGTAACACCACAAAGAGATAAGTCAGTGGTA
+TGTGGGAGTTTGTTTCATACACCAAAGTTTGTGAAGGGTCGTCAGACACCAAAACATATT
+TCTGAAAGTCTAGGAGCTGAGGTGGATCCTGATATGTCTTGGTCAAGTTCTTTAGCTACA
+CCACCCACCCTTAGTTCTACTGTGCTCATAGTCAGAAATGAAGAAGCATCTGAAACTGTA
+TTTCCTCATGATACTACTGCTAATGTGAAAAGCTATTTTTCCAATCATGATGAAAGTCTG
+AAGAAAAATGATAGATTTATCGCTTCTGTGACAGACAGTGAAAACACAAATCAAAGAGAA
+GCTGCAAGTCATGGATTTGGAAAAACATCAGGGAATTCATTTAAAGTAAATAGCTGCAAA
+GACCACATTGGAAAGTCAATGCCAAATGTCCTAGAAGATGAAGTATATGAAACAGTTGTA
+GATACCTCTGAAGAAGATAGTTTTTCATTATGTTTTTCTAAATGTAGAACAAAAAATCTA
+CAAAAAGTAAGAACTAGCAAGACTAGGAAAAAAATTTTCCATGAAGCAAACGCTGATGAA
+TGTGAAAAATCTAAAAACCAAGTGAAAGAAAAATACTCATTTGTATCTGAAGTGGAACCA
+AATGATACTGATCCATTAGATTCAAATGTAGCAAATCAGAAGCCCTTTGAGAGTGGAAGT
+GACAAAATCTCCAAGGAAGTTGTACCGTCTTTGGCCTGTGAATGGTCTCAACTAACCCTT
+TCAGGTCTAAATGGAGCCCAGATGGAGAAAATACCCCTATTGCATATTTCTTCATGTGAC
+CAAAATATTTCAGAAAAAGACCTATTAGACACAGAGAACAAAAGAAAGAAAGATTTTCTT
+ACTTCAGAGAATTCTTTGCCACGTATTTCTAGCCTACCAAAATCAGAGAAGCCATTAAAT
+GAGGAAACAGTGGTAAATAAGAGAGATGAAGAGCAGCATCTTGAATCTCATACAGACTGC
+ATTCTTGCAGTAAAGCAGGCAATATCTGGAACTTCTCCAGTGGCTTCTTCATTTCAGGGT
+ATCAAAAAGTCTATATTCAGAATAAGAGAATCACCTAAAGAGACTTTCAATGCAAGTTTT
+TCAGGTCATATGACTGATCCAAACTTTAAAAAAGAAACTGAAGCCTCTGAAAGTGGACTG
+GAAATACATACTGTTTGCTCACAGAAGGAGGACTCCTTATGTCCAAATTTAATTGATAAT
+GGAAGCTGGCCAGCCACCACCACACAGAATTCTGTAGCTTTGAAGAATGCAGGTTTAATA
+TCCACTTTGAAAAAGAAAACAAATAAGTTTATTTATGCTATACATGATGAAACATCTTAT
+AAAGGAAAAAAAATACCGAAAGACCAAAAATCAGAACTAATTAACTGTTCAGCCCAGTTT
+GAAGCAAATGCTTTTGAAGCACCACTTACATTTGCAAATGCTGATTCAGGTTTATTGCAT
+TCTTCTGTGAAAAGAAGCTGTTCACAGAATGATTCTGAAGAACCAACTTTGTCCTTAACT
+AGCTCTTTTGGGACAATTCTGAGGAAATGTTCTAGAAATGAAACATGTTCTAATAATACA
+GTAATCTCTCAGGATCTTGATTATAAAGAAGCAAAATGTAATAAGGAAAAACTACAGTTA
+TTTATTACCCCAGAAGCTGATTCTCTGTCATGCCTGCAGGAAGGACAGTGTGAAAATGAT
+CCAAAAAGCAAAAAAGTTTCAGATATAAAAGAAGAGGTCTTGGCTGCAGCATGTCACCCA
+GTACAACATTCAAAAGTGGAATACAGTGATACTGACTTTCAATCCCAGAAAAGTCTTTTA
+TATGATCATGAAAATGCCAGCACTCTTATTTTAACTCCTACTTCCAAGGATGTTCTGTCA
+AACCTAGTCATGATTTCTAGAGGCAAAGAATCATACAAAATGTCAGACAAGCTCAAAGGT
+AACAATTATGAATCTGATGTTGAATTAACCAAAAATATTCCCATGGAAAAGAATCAAGAT
+GTATGTGCTTTAAATGAAAATTATAAAAACGTTGAGCTGTTGCCACCTGAAAAATACATG
+AGAGTAGCATCACCTTCAAGAAAGGTACAATTCAACCAAAACACAAATCTAAGAGTAATC
+CAAAAAAATCAAGAAGAAACTACTTCAATTTCAAAAATAACTGTCAATCCAGACTCTGAA
+GAACTTTTCTCAGACAATGAGAATAATTTTGTCTTCCAAGTAGCTAATGAAAGGAATAAT
+CTTGCTTTAGGAAATACTAAGGAACTTCATGAAACAGACTTGACTTGTGTAAACGAACCC
+ATTTTCAAGAACTCTACCATGGTTTTATATGGAGACACAGGTGATAAACAAGCAACCCAA
+GTGTCAATTAAAAAAGATTTGGTTTATGTTCTTGCAGAGGAGAACAAAAATAGTGTAAAG
+CAGCATATAAAAATGACTCTAGGTCAAGATTTAAAATCGGACATCTCCTTGAATATAGAT
+AAAATACCAGAAAAAAATAATGATTACATGAACAAATGGGCAGGACTCTTAGGTCCAATT
+TCAAATCACAGTTTTGGAGGTAGCTTCAGAACAGCTTCAAATAAGGAAATCAAGCTCTCT
+GAACATAACATTAAGAAGAGCAAAATGTTCTTCAAAGATATTGAAGAACAATATCCTACT
+AGTTTAGCTTGTGTTGAAATTGTAAATACCTTGGCATTAGATAATCAAAAGAAACTGAGC
+AAGCCTCAGTCAATTAATACTGTATCTGCACATTTACAGAGTAGTGTAGTTGTTTCTGAT
+TGTAAAAATAGTCATATAACCCCTCAGATGTTATTTTCCAAGCAGGATTTTAATTCAAAC
+CATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAA
+TCAGGAAGTCAGTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGT
+ACATTTGAAGTGCCTGAAAACCAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGA
+GATGCTGATCTTCATGTCATAATGAATGCCCCATCGATTGGTCAGGTAGACAGCAGCAAG
+CAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGGCCTGTTGAAAAATGACTGT
+AACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGGGGCTTTTAT
+TCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTG
+TTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTA
+TCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGAT
+AAAACTGTAAGTGAAAAAAATAATAAATGCCAACTGATATTACAAAATAATATTGAAATG
+ACTACTGGCACTTTTGTTGAAGAAATTACTGAAAATTACAAGAGAAATACTGAAAATGAA
+GATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTTAGAATTTGATGGCAGTGAT
+TCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTATTTACTGAT
+CAGCACAACATATGTCTTAAATTATCTGGCCAGTTTATGAAGGAGGGAAACACTCAGATT
+AAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCAT
+GGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGAT
+TTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAA
+GAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTT
+TCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTAT
+GAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGA
+AATCAACTAGTGACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCAAAGAACCTACT
+CTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGAC
+AAAGTGAAAAACCTTTTTGATGAAAAAGAGCAAGGTACTAGTGAAATCACCAGTTTTAGC
+CATCAATGGGCAAAGACCCTAAAGTACAGAGAGGCCTGTAAAGACCTTGAATTAGCATGT
+GAGACCATTGAGATCACAGCTGCCCCAAAGTGTAAAGAAATGCAGAATTCTCTCAATAAT
+GATAAAAACCTTGTTTCTATTGAGACTGTGGTGCCACCTAAGCTCTTAAGTGATAATTTA
+TGTAGACAAACTGAAAATCTCAAAACATCAAAAAGTATCTTTTTGAAAGTTAAAGTACAT
+GAAAATGTAGAAAAAGAAACAGCAAAAAGTCCTGCAACTTGTTACACAAATCAGTCCCCT
+TATTCAGTCATTGAAAATTCAGCCTTAGCTTTTTACACAAGTTGTAGTAGAAAAACTTCT
+GTGAGTCAGACTTCATTACTTGAAGCAAAAAAATGGCTTAGAGAAGGAATATTTGATGGT
+CAACCAGAAAGAATAAATACTGCAGATTATGTAGGAAATTATTTGTATGAAAATAATTCA
+AACAGTACTATAGCTGAAAATGACAAAAATCATCTCTCCGAAAAACAAGATACTTATTTA
+AGTAACAGTAGCATGTCTAACAGCTATTCCTACCATTCTGATGAGGTATATAATGATTCA
+GGATATCTCTCAAAAAATAAACTTGATTCTGGTATTGAGCCAGTATTGAAGAATGTTGAA
+GATCAAAAAAACACTAGTTTTTCCAAAGTAATATCCAATGTAAAAGATGCAAATGCATAC
+CCACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGC
+AAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGG
+CCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAA
+AAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAAT
+AAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTACGAGGCATTGGATGATTCA
+GAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCACATAAGGTT
+TTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAG
+AAAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGT
+AGTATAGGGAAGCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACA
+GCAAGTGGAAAATCTGTCCAGGTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTT
+TCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAA
+CATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATA
+TCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACA
+GCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTA
+GAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAA
+AATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCA
+GAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGT
+GGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAA
+GACAAACAACAGTTGGTATTAGGAACCAAAGTCTCACTTGTTGAGAACATTCATGTTTTG
+GGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTT
+TCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAA
+AACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTG
+ACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAG
+GAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTG
+GGAGAACCCTCAATCAAAAGAAACTTATTAAATGAATTTGACAGGATAATAGAAAATCAA
+GAAAAATCCTTAAAGGCTTCAAAAAGCACTCCAGATGGCACAATAAAAGATCGAAGATTG
+TTTATGCATCATGTTTCTTTAGAGCCGATTACCTGTGTACCCTTTCGCACAACTAAGGAA
+CGTCAAGAGATACAGAATCCAAATTTTACCGCACCTGGTCAAGAATTTCTGTCTAAATCT
+CATTTGTATGAACATCTGACTTTGGAAAAATCTTCAAGCAATTTAGCAGTTTCAGGACAT
+CCATTTTATCAAGTTTCTGCTACAAGAAATGAAAAAATGAGACACTTGATTACTACAGGC
+AGACCAACCAAAGTCTTTGTTCCACCTTTTAAAACTAAATCACATTTTCACAGAGTTGAA
+CAGTGTGTTAGGAATATTAACTTGGAGGAAAACAGACAAAAGCAAAACATTGATGGACAT
+GGCTCTGATGATAGTAAAAATAAGATTAATGACAATGAGATTCATCAGTTTAACAAAAAC
+AACTCCAATCAAGCAGCAGCTGTAACTTTCACAAAGTGTGAAGAAGAACCTTTAGATTTA
+ATTACAAGTCTTCAGAATGCCAGAGATATACAGGATATGCGAATTAAGAAGAAACAAAGG
+CAACGCGTCTTTCCACAGCCAGGCAGTCTGTATCTTGCAAAAACATCCACTCTGCCTCGA
+ATCTCTCTGAAAGCAGCAGTAGGAGGCCAAGTTCCCTCTGCGTGTTCTCATAAACAGCTG
+TATACGTATGGCGTTTCTAAACATTGCATAAAAATTAACAGCAAAAATGCAGAGTCTTTT
+CAGTTTCACACTGAAGATTATTTTGGTAAGGAAAGTTTATGGACTGGAAAAGGAATACAG
+TTGGCTGATGGTGGATGGCTCATACCCTCCAATGATGGAAAGGCTGGAAAAGAAGAATTT
+TATAGGGCTCTGTGTGACACTCCAGGTGTGGATCCAAAGCTTATTTCTAGAATTTGGGTT
+TATAATCACTATAGATGGATCATATGGAAACTGGCAGCTATGGAATGTGCCTTTCCTAAG
+GAATTTGCTAATAGATGCCTAAGCCCAGAAAGGGTGCTTCTTCAACTAAAATACAGATAT
+GATACGGAAATTGATAGAAGCAGAAGATCGGCTATAAAAAAGATAATGGAAAGGGATGAC
+ACAGCTGCAAAAACACTTGTTCTCTGTGTTTCTGACATAATTTCATTGAGCGCAAATATA
+TCTGAAACTTCTAGCAATAAAACTAGTAGTGCAGATACCCAAAAAGTGGCCATTATTGAA
+CTTACAGATGGGTGGTATGCTGTTAAGGCCCAGTTAGATCCTCCCCTCTTAGCTGTCTTA
+AAGAATGGCAGACTGACAGTTGGTCAGAAGATTATTCTTCATGGAGCAGAACTGGTGGGC
+TCTCCTGATGCCTGTACACCTCTTGAAGCCCCAGAATCTCTTATGTTAAAGATTTCTGCT
+AACAGTACTCGGCCTGCTCGCTGGTATACCAAACTTGGATTCTTTCCTGACCCTAGACCT
+TTTCCTCTGCCCTTATCATCGCTTTTCAGTGATGGAGGAAATGTTGGTTGTGTTGATGTA
+ATTATTCAAAGAGCATACCCTATACAGTGGATGGAGAAGACATCATCTGGATTATACATA
+TTTCGCAATGAAAGAGAGGAAGAAAAGGAAGCAGCAAAATATGTGGAGGCCCAACAAAAG
+AGACTAGAAGCCTTATTCACTAAAATTCAGGAGGAATTTGAAGAACATGAAGAAAACACA
+ACAAAACCATATTTACCATCACGTGCACTAACAAGACAGCAAGTTCGTGCTTTGCAAGAT
+GGTGCAGAGCTTTATGAAGCAGTGAAGAATGCAGCAGACCCAGCTTACCTTGAGGGTTAT
+TTCAGTGAAGAGCAGTTAAGAGCCTTGAATAATCACAGGCAAATGTTGAATGATAAGAAA
+CAAGCTCAGATCCAGTTGGAAATTAGGAAGGCCATGGAATCTGCTGAACAAAAGGAACAA
+GGTTTATCAAGGGATGTCACAACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAA
+GAAAAAGATTCAGTTATACTGAGTATTTGGCGTCCATCATCAGATTTATATTCTCTGTTA
+ACAGAAGGAAAGAGATACAGAATTTATCATCTTGCAACTTCAAAATCTAAAAGTAAATCT
+GAAAGAGCTAACATACAGTTAGCAGCGACAAAAAAAACTCAGTATCAACAACTACCGGTT
+TCAGATGAAATTTTATTTCAGATTTACCAGCCACGGGAGCCCCTTCACTTCAGCAAATTT
+TTAGATCCAGACTTTCAGCCATCTTGTTCTGAGGTGGACCTAATAGGATTTGTCGTTTCT
+GTTGTGAAAAAAACAGGACTTGCCCCTTTCGTCTATTTGTCAGACGAATGTTACAATTTA
+CTGGCAATAAAGTTTTGGATAGACCTTAATGAGGACATTATTAAGCCTCATATGTTAATT
+GCTGCAAGCAACCTCCAGTGGCGACCAGAATCCAAATCAGGCCTTCTTACTTTATTTGCT
+GGAGATTTTTCTGTGTTTTCTGCTAGTCCAAAAGAGGGCCACTTTCAAGAGACATTCAAC
+AAAATGAAAAATACTGTTGAGAATATTGACATACTTTGCAATGAAGCAGAAAACAAGCTT
+ATGCATATACTGCATGCAAATGATCCCAAGTGGTCCACCCCAACTAAAGACTGTACTTCA
+GGGCCGTACACTGCTCAAATCATTCCTGGTACAGGAAACAAGCTTCTGATGTCTTCTCCT
+AATTGTGAGATATATTATCAAAGTCCTTTATCACTTTGTATGGCCAAAAGGAAGTCTGTT
+TCCACACCTGTCTCAGCCCAGATGACTTCAAAGTCTTGTAAAGGGGAGAAAGAGATTGAT
+GACCAAAAGAACTGCAAAAAGAGAAGAGCCTTGGATTTCTTGAGTAGACTGCCTTTACCT
+CCACCTGTTAGTCCCATTTGTACATTTGTTTCTCCGGCTGCACAGAAGGCATTTCAGCCA
+CCAAGGAGTTGTGGCACCAAATACGAAACACCCATAAAGAAAAAAGAACTGAATTCTCCT
+CAGATGACTCCATTTAAAAAATTCAATGAAATTTCTCTTTTGGAAAGTAATTCAATAGCT
+GACGAAGAACTTGCATTGATAAATACCCAAGCTCTTTTGTCTGGTTCAACAGGAGAAAAA
+CAATTTATATCTGTCAGTGAATCCACTAGGACTGCTCCCACCAGTTCAGAAGATTATCTC
+AGACTGAAACGACGTTGTACTACATCTCTGATCAAAGAACAGGAGAGTTCCCAGGCCAGT
+ACGGAAGAATGTGAGAAAAATAAGCAGGACACAATTACAACTAAAAAATATATCTAA
+>Gene02
+ATGCTGCTGCTGGCGAGATGTCTGCTGCTAGTCCTCGTCTCCTCGCTGCTGGTATGCTCGGGACTGGCGT
+GCGGACCGGGCAGGGGGTTCGGGAAGAGGAGGCACCCCAAAAAGCTGACCCCTTTAGCCTACAAGCAGTT
+TATCCCCAATGTGGCCGAGAAGACCCTAGGCGCCAGCGGAAGGTATGAAGGGAAGATCTCCAGAAACTCC
+GAGCGATTTAAGGAACTCACCCCCAATTACAACCCCGACATCATATTTAAGGATGAAGAAAACACCGGAG
+CGGACAGGCTGATGACTCAGAGGTGTAAGGACAAGTTGAACGCTTTGGCCATCTCGGTGATGAACCAGTG
+GCCAGGAGTGAAACTGCGGGTGACCGAGGGCTGGGACGAAGATGGCCACCACTCAGAGGAGTCTCTGCAC
+TACGAGGGCCGCGCAGTGGACATCACCACGTCTGACCGCGACCGCAGCAAGTACGGCATGCTGGCCCGCC
+TGGCGGTGGAGGCCGGCTTCGACTGGGTGTACTACGAGTCCAAGGCACATATCCACTGCTCGGTGAAAGC
+AGAGAACTCGGTGGCGGCCAAATCGGGAGGCTGCTTCCCGGGCTCGGCCACGGTGCACCTGGAGCAGGGC
+GGCACCAAGCTGGTGAAGGACCTGAGCCCCGGGGACCGCGTGCTGGCGGCGGACGACCAGGGCCGGCTGC
+TCTACAGCGACTTCCTCACTTTCCTGGACCGCGACGACGGCGCCAAGAAGGTCTTCTACGTGATCGAGAC
+GCGGGAGCCGCGCGAGCGCCTGCTGCTCACCGCCGCGCACCTGCTCTTTGTGGCGCCGCACAACGACTCG
+GCCACCGGGGAGCCCGAGGCGTCCTCGGGCTCGGGGCCGCCTTCCGGGGGCGCACTGGGGCCTCGGGCGC
+TGTTCGCCAGCCGCGTGCGCCCGGGCCAGCGCGTGTACGTGGTGGCCGAGCGTGACGGGGACCGCCGGCT
+CCTGCCCGCCGCTGTGCACAGCGTGACCCTAAGCGAGGAGGCCGCGGGCGCCTACGCGCCGCTCACGGCC
+CAGGGCACCATTCTCATCAACCGGGTGCTGGCCTCGTGCTACGCGGTCATCGAGGAGCACAGCTGGGCGC
+ACCGGGCCTTCGCGCCCTTCCGCCTGGCGCACGCGCTCCTGGCTGCACTGGCGCCCGCGCGCACGGACCG
+CGGCGGGGACAGCGGCGGCGGGGACCGCGGGGGCGGCGGCGGCAGAGTAGCCCTAACCGCTCCAGGTGCT
+GCCGACGCTCCGGGTGCGGGGGCCACCGCGGGCATCCACTGGTACTCGCAGCTGCTCTACCAAATAGGCA
+CCTGGCTCCTGGACAGCGAGGCCCTGCACCCGCTGGGCATGGCGGTCAAGTCCAGCTGA
+>Gene03
+ATGGAGAAAAAGGGTTTGGTGAGCAACAGCTTGAAAGATCATGCTGGTATTGTCACCAGA
+GCCATTAGGCGCAGCAAGACTACCTATGAAGAAGACGATTACAATTTTGATGGGTTTGCA
+TGGCCTCCAAGATCTTACACGTGTAGCTTCTGCAAAAGGGAATTTAGATCTGCTCAAGCT
+CTTGGCGGCCACATGAATGTTCACCGAAAAGACCGAGCCAGGCTCAAAGGCTCACCCCCA
+AGAGACAGTCAATACACGAGTACTATTCTTAACCTTAACCTCAACAAAGTGCCAAACCCT
+AACCCTAATTTCTCATCAACATCATCAGCATCCTCACCATCCTCACCATCCTCCTGGATA
+TCACCAATTAGTAGCACATTACCCTCTTTGATATCACCACCAGCTCCTCCACCTGTTTTT
+TTGGTGCCGTCTAGCGAAAATATGAAATGGGTTGTGGGAGACACCCTCTTTAATCACCCT
+CTAAACTTCAAAGCCTCGGATTTTGGTACTACAGTAAAGAAGAACGCAGAATCTTTTTGT
+GGAGTAGGAGATCGTCAATGTGATGGTTTCATTGGAGAAGAACATGGGTGCATAAAGACT
+GTCAAGGCAGCTGATCATCCTCATCATCCGATTGTTAGGTTGGACTTGGAGATCGGTATG
+CTTGGTGACTCAAATAAGGAAGACTTAGATTTGGAACTTCGATTGGGATACTCTTAG
diff --git a/tests/data/mamut.descriptions.txt b/tests/data/mamut.descriptions.txt
@@ -0,0 +1,3 @@
+Gene01	Breast Cancer 2 gene, fingers crossed you've got good alleles for this one!
+Gene02	SonicHedgehog, the gene not the adorable blue video game mascot
+Gene03	Superman class transcription factor
diff --git a/tests/data/mamut.xref.txt b/tests/data/mamut.xref.txt
@@ -0,0 +1,7 @@
+Gene01	BRCA2	Ensembl	http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32315474-32400266
+Gene02	SonicHedgehog	Ensembl	http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690;r=7:155799986-155812273
+Gene03	Superman	Plaza	http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/genes/view/MD13G022660
+Gene01	BRCA2	token	
+Gene02	SHH	token	
+Gene02	SonicHedgehog	token	
+Gene03	Superman	token	
diff --git a/tests/data/test_go.obo b/tests/data/test_go.obo
@@ -0,0 +1,50 @@
+format-version: 1.2
+data-version: releases/2014-10-14
+date: 13:10:2014 08:33
+saved-by: kmv
+auto-generated-by: TermGenie 1.0
+subsetdef: Cross_product_review "Involved_in"
+subsetdef: goantislim_grouping "Grouping classes that can be excluded"
+subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
+subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
+subsetdef: goslim_aspergillus "Aspergillus GO slim"
+subsetdef: goslim_candida "Candida GO slim"
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_goa "GOA and proteome slim"
+subsetdef: goslim_metagenomics "Metagenomics GO slim"
+subsetdef: goslim_pir "PIR GO slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_pombe "Fission yeast GO slim"
+subsetdef: goslim_virus "Viral GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
+subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
+subsetdef: virus_checked "Viral overhaul terms"
+synonymtypedef: systematic_synonym "Systematic synonym" EXACT
+default-namespace: gene_ontology
+remark: cvs version: $Revision: 21018 $
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0]
+ontology: go
+property_value: propformat-version "1.2" xsd:string
+
+[Term]
+id: GO:0000001
+name: top_label
+namespace: biological_process
+def: "Top GO LABEL"
+synonym: "top_level" EXACT []
+
+[Term]
+id: GO:0000002
+name: second_label
+namespace: biological_process
+def: "Second label"
+is_a: GO:0000001 ! top_label
+
+[Term]
+id: GO:0000003
+name: third_label
+namespace: biological_process
+def: "Third label"
+is_a: GO:0000001 ! top_label
diff --git a/utils/entropy.py b/utils/entropy.py
@@ -1,6 +1,7 @@
 from math import log2
 from bisect import bisect
 
+
 def entropy(dist):
     """
     Calculates the entropy for a given distribution (!)