From 52724cc888e5aad6cf69a68c530efe0ec4e45f58 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 1 Aug 2014 17:03:20 +0200
Subject: [PATCH] Fixed empty allele bug.
---
mutalyzer/describe.py | 2 ++
tests/test_describe.py | 22 +++++++++-------------
2 files changed, 11 insertions(+), 13 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 55589466..c76ff4c4 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -624,6 +624,8 @@ def describe_dna(s1, s2):
#if
#for
+ if not description:
+ return Allele([DNAVar()])
return description
#describe_dna
diff --git a/tests/test_describe.py b/tests/test_describe.py
index f1ccb618..080f3716 100644
--- a/tests/test_describe.py
+++ b/tests/test_describe.py
@@ -25,7 +25,7 @@ class TestDescribe(MutalyzerTest):
"""
reference = "ACGTCGATTCGCTAGCTTCGGGGGATAGATAGAGATATAGAGAT"
- result = describe.describe(reference, sample)
+ result = describe.describe_dna(reference, sample)
assert result[0].type == expected[0]
assert result[0].start == expected[1]
assert result[0].end == expected[2]
@@ -39,41 +39,37 @@ class TestDescribe(MutalyzerTest):
"""
Test 1.
"""
- result = describe.describe(
+ result = describe.describe_dna(
'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA',
'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA')
- description = describe.allele_description(result)
- assert description == '[5_6insTT;17del;26A>C;35dup]'
+ assert unicode(result) == '[5_6insTT;17del;26A>C;35dup]'
def test2(self):
"""
Test 2.
"""
- result = describe.describe(
+ result = describe.describe_dna(
'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTACTGTG',
'TAAGCACCAGGAGTCCATGAAGAAGCTGGATCCTCCCATGGAATCCCCTACTCTACTGTG')
- description = describe.allele_description(result)
- assert description == '[26A>C;30C>A;35G>C]'
+ assert unicode(result) == '[26A>C;30C>A;35G>C]'
def test3(self):
"""
Test 3.
"""
- result = describe.describe(
+ result = describe.describe_dna(
'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTA',
'TAAGCACCAGGAGTCCATGAAGAAGCCATGTCCTGCCATGGAATCCCCTACTCTA')
- description = describe.allele_description(result)
- assert description == '[26_29inv;30C>G]'
+ assert unicode(result) == '[26_29inv;30C>G]'
def test4(self):
"""
Test 4.
"""
- result = describe.describe(
+ result = describe.describe_dna(
'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTA',
'TAAGCACCAGGAGTCCATGAAGAAGCCATGTCCTGCCATGAATCCCCTACTCTA')
- description = describe.allele_description(result)
- assert description == '[26_29inv;30C>G;41del]'
+ assert unicode(result) == '[26_29inv;30C>G;41del]'
def test5(self):
"""
--
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