"""
Tests for the mapping module.
"""
from utils import TEST_SETTINGS
from mutalyzer.config import settings
settings.configure(TEST_SETTINGS)
#import logging; logging.basicConfig()
from nose.tools import *
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
class TestConverter():
"""
Test the Converter class.
"""
def setUp(self):
"""
Initialize test converter module.
"""
self.output = Output(__file__)
def _converter(self, build):
"""
Create a Converter instance for a given build.
"""
return Converter(build, self.output)
def test_converter(self):
"""
Simple test.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.274G>T')
assert_equal(genomic, 'NC_000011.9:g.111959695G>T')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.274G>T' in coding
# Fix for r536: disable the -u and +d convention.
#assert 'NR_028383.1:c.1-u2173C>A' in coding
assert 'NR_028383.1:n.-2173C>A' in coding
def test_converter_non_coding(self):
"""
Test with variant on non-coding transcript.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NR_028383.1:n.-2173C>A')
assert_equal(genomic, 'NC_000011.9:g.111959695G>T')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.274G>T' in coding
# Fix for r536: disable the -u and +d convention.
#assert 'NR_028383.1:c.1-u2173C>A' in coding
assert 'NR_028383.1:n.-2173C>A' in coding
def test_converter_compound(self):
"""
Test with compound variant.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.[274G>T;278A>G]')
assert_equal(genomic, 'NC_000011.9:g.[111959695G>T;111959699A>G]')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.[274G>T;278A>G]' in coding
assert 'NR_028383.1:n.[-2173C>A;-2177T>C]' in coding
def test_hla_cluster(self):
"""
Convert to primary assembly.
Transcript NM_000500.5 is mapped to different chromosome locations,
but we like to just see the primary assembly mapping to chromosome 6.
See also bug #58.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_000500.5:c.92C>T')
assert_equal(genomic, 'NC_000006.11:g.32006291C>T')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_000500.5:c.92C>T' in coding
def test_converter_del_length_reverse(self):
"""
Position converter on deletion (denoted by length) on transcripts
located on the reverse strand.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000022.10:g.51016285_51017117del123456789', 'list')
# Fix for r536: disable the -u and +d convention.
#assert 'NM_001145134.1:c.-138-u21_60del123456789' in coding
#assert 'NR_021492.1:c.1-u5170_1-u4338del123456789' in coding
assert 'NM_001145134.1:c.-159_60del123456789' in coding
assert 'NR_021492.1:n.-5170_-4338del123456789' in coding
def test_S_Venkata_Suresh_Kumar(self):
"""
Test for correct mapping information on genes where CDS start or stop
is exactly on the border of an exon.
Bug reported February 24, 2012 by S Venkata Suresh Kumar.
Note: You need the full hg18 and hg19 databases for these tests to
pass (i.e. the one used on the production server, possibly
updated with newer mappings from the NCBI).
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000001.10:g.115259837_115259837delT', 'list')
assert 'NM_001007553.1:c.3863delA' not in coding
assert 'NM_001007553.2:c.3863delA' not in coding
assert 'NM_001007553.1:c.*953delA' in coding
assert 'NM_001130523.1:c.*953delA' in coding
assert 'NM_001007553.2:c.*953delA' in coding
assert 'NM_001130523.2:c.*953delA' in coding
def test_S_Venkata_Suresh_Kumar_more(self):
"""
Another test for correct mapping information on genes where CDS start
or stop is exactly on the border of an exon.
Bug reported March 21, 2012 by S Venkata Suresh Kumar.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000001.10:g.160012314_160012329del16', 'list')
assert 'NM_002241.4:c.-27250-7_-27242del16' not in coding
#assert 'NM_002241.3:c.-27340-7_-27332del16' not in coding
assert 'NM_002241.4:c.1-7_9del16' in coding
#assert 'NM_002241.3:c.1-7_9del16' in coding
def test_range_order_forward_correct(self):
"""
Just a normal position converter call, both directions. See Trac #95.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.-1_274del')
assert_equal(genomic, 'NC_000011.9:g.111957631_111959695del')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.-1_274del' in coding
def test_range_order_forward_incorrect_c2chrom(self):
"""
Incorrect order of a range on the forward strand. See Trac #95.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.274_-1del')
assert_equal(genomic, None)
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert_equal(len(erange), 1)
def test_range_order_reverse_correct(self):
"""
Just a normal position converter call on the reverse strand, both
directions. See Trac #95.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_001162505.1:c.-1_40del')
assert_equal(genomic, 'NC_000020.10:g.48770135_48770175del')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_001162505.1:c.-1_40del' in coding
def test_range_order_reverse_incorrect_c2chrom(self):
"""
Incorrect order of a range on the reverse strand. See Trac #95.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_001162505.1:c.40_-1del')
assert_equal(genomic, None)
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert_equal(len(erange), 1)
def test_range_order_incorrect_chrom2c(self):
"""
Incorrect order of a chromosomal range. See Trac #95.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000011.9:g.111959695_111957631del', 'list')
assert_equal(coding, None)
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert_equal(len(erange), 1)
def test_delins_large_ins_c2chrom(self):
"""
Delins with multi-base insertion c. to chrom.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.274delinsTAAA')
assert_equal(genomic, 'NC_000011.9:g.111959695delinsTAAA')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.274delinsTAAA' in coding
def test_delins_large_ins_explicit_c2chrom(self):
"""
Delins with multi-base insertion and explicit deleted sequence c. to chrom.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.274delGinsTAAA')
assert_equal(genomic, 'NC_000011.9:g.111959695delinsTAAA')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_003002.2:c.274delinsTAAA' in coding
def test_delins_large_ins_chrom2c(self):
"""
Delins with multi-base insertion chrom to c.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000011.9:g.111959695delinsTAAA', 'list')
assert 'NM_003002.2:c.274delinsTAAA' in coding
def test_delins_large_ins_explicit_chrom2c(self):
"""
Delins with multi-base insertion and explicit deleted sequence chrom to c.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000011.9:g.111959695delGinsTAAA', 'list')
assert 'NM_003002.2:c.274delinsTAAA' in coding
def test_chrm_chrom2c(self):
"""
Mitochondrial m. to c.
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_012920.1:m.12030del', 'list')
assert 'NC_012920.1(ND4_v001):c.1271del' in coding
def test_chrm_name_chrom2c(self):
"""
Mitochondrial m. (by chromosome name) to c.
"""
converter = self._converter('hg19')
variant = converter.correctChrVariant('chrM:m.12030del')
coding = converter.chrom2c(variant, 'list')
assert 'NC_012920.1(ND4_v001):c.1271del' in coding
def test_chrm_c2chrom(self):
"""
Mitochondrial c. to m.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NC_012920.1(ND4_v001):c.1271del')
assert_equal(genomic, 'NC_012920.1:m.12030del')
def test_nm_without_selector_chrom2c(self):
"""
NM reference without transcript selection c. to g.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2:c.109A>T')
assert_equal(genomic, 'NC_000008.10:g.61654100A>T')
def test_nm_with_selector_chrom2c(self):
"""
NM reference with transcript selection c. to g.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2(CHD7_v001):c.109A>T')
assert_equal(genomic, 'NC_000008.10:g.61654100A>T')
def test_nm_c2chrom_no_selector(self):
"""
To NM reference should never result in transcript selection.
"""
converter = self._converter('hg19')
variant = converter.correctChrVariant('NC_000008.10:g.61654100A>T')
coding = converter.chrom2c(variant, 'list')
assert 'NM_017780.2:c.109A>T' in coding
def test_incorrect_selector_c2chrom(self):
"""
Incorrect selector.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2(CHD8):c.109A>T')
erange = self.output.getMessagesWithErrorCode('EACCNOTINDB')
assert_equal(len(erange), 1)
def test_incorrect_selector_version_c2chrom(self):
"""
Incorrect selector version.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2(CHD7_v002):c.109A>T')
erange = self.output.getMessagesWithErrorCode('EACCNOTINDB')
assert_equal(len(erange), 1)
def test_no_selector_version_c2chrom(self):
"""
Selector but no selector version.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2(CHD7):c.109A>T')
assert_equal(genomic, 'NC_000008.10:g.61654100A>T')
def test_incorrect_selector_no_selector_version_c2chrom(self):
"""
Incorrect selector, no selector version.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_017780.2(CHD8):c.109A>T')
erange = self.output.getMessagesWithErrorCode('EACCNOTINDB')
assert_equal(len(erange), 1)