From 80cbca6263fbf6a348584d89b5152f426b242d39 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 29 Mar 2012 09:31:49 +0000
Subject: [PATCH] More Crossmap tests
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@501 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
tests/test_crossmap.py | 37 +++++++++++++++++++++++++------------
1 file changed, 25 insertions(+), 12 deletions(-)
diff --git a/tests/test_crossmap.py b/tests/test_crossmap.py
index 2350695e..ce3d81d4 100644
--- a/tests/test_crossmap.py
+++ b/tests/test_crossmap.py
@@ -256,33 +256,46 @@ class TestCrossmap():
assert_equal(cm.tuple2string(cm.g2x(2123)), '-156-u23752936')
assert_equal(cm.tuple2string(cm.g2x(2124)), '-156-u23752935')
- def test_cds_start_on_splice_site_more(self):
+ def test_cds_start_on_splice_site_reverse(self):
"""
- Test a gene some more that has a CDS that starts on an exon splice
- site.
+ Test a gene on the reverse strand that has a CDS that starts on an
+ exon splice site.
"""
- rna = [23755059, 23755214, 23777833, 23778028, 23808749, 23808851, 23824768,
- 23824856, 23853497, 23853617, 23869553, 23869626, 23894775, 23894899,
+ rna = [23777833, 23778028, 23808749, 23808851, 23824768, 23824856,
+ 23853497, 23853617, 23869553, 23869626, 23894775, 23894899,
23898506, 23899304]
+ cds = [23755214, 23778028]
+ cm = Crossmap(rna, cds, -1)
+ assert_equal(cm._Crossmap__crossmapping,
+ [196, 1, -1, -103, -104, -192, -193, -313, -314, -387,
+ -388, -512, -513, -1311])
+
+ def test_cds_start_on_splice_site_other(self):
+ """
+ Test a gene that has a CDS that starts on an other exon splice site.
+ """
+ rna = [23755059, 23755214, 23777833, 23778028, 23808749, 23808851,
+ 23824768, 23824856, 23853497, 23853617, 23869553, 23869626,
+ 23894775, 23894899, 23898506, 23899304]
cds = [23755214, 23898680]
cm = Crossmap(rna, cds, 1)
assert_equal(cm._Crossmap__crossmapping,
- [-155, 1, 2, 197, 198, 300, 301, 389, 390,
- 510, 511, 584, 585, 709, 710, 1508])
+ [-155, 1, 2, 197, 198, 300, 301, 389, 390, 510, 511, 584,
+ 585, 709, 710, 1508])
- def test_cds_start_on_splice_site_reverse(self):
+ def test_cds_start_on_splice_site_other_reverse(self):
"""
Test a gene on the reverse strand that has a CDS that starts on an
- exon splice site.
+ other exon splice site.
"""
rna = [23777833, 23778028, 23808749, 23808851, 23824768, 23824856,
23853497, 23853617, 23869553, 23869626, 23894775, 23894899,
23898506, 23899304]
- cds = [23755214, 23778028]
+ cds = [23755214, 23808749]
cm = Crossmap(rna, cds, -1)
assert_equal(cm._Crossmap__crossmapping,
- [196, 1, -1, -103, -104, -192, -193, -313, -314, -387,
- -388, -512, -513, -1311])
+ [197, 2, 1, -102, -103, -191, -192, -312, -313, -386,
+ -387, -511, -512, -1310])
def test_cds_start_on_transcript_start(self):
"""
--
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