"""
Tests for the mapping module.
"""
from __future__ import unicode_literals
#import logging; logging.basicConfig()
from sqlalchemy import or_
from mutalyzer.db.models import Assembly
from mutalyzer.output import Output
from mutalyzer.mapping import Converter
from fixtures import database, hg19, hg19_transcript_mappings
from utils import MutalyzerTest
class TestConverter(MutalyzerTest):
"""
Test the Converter class.
"""
fixtures = (database, hg19, hg19_transcript_mappings)
def setup(self):
super(TestConverter, self).setup()
self.output = Output(__file__)
def _converter(self, assembly_name_or_alias):
"""
Create a Converter instance for a given genome assembly.
"""
assembly = Assembly.query \
.filter(or_(Assembly.name == assembly_name_or_alias,
Assembly.alias == assembly_name_or_alias)) \
.one()
return Converter(assembly, self.output)
def test_converter(self):
"""
Simple test.
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_003002.2:c.274G>T')
assert 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 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 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.
"""
# Todo: This test is bogus now that we use a fixture that has just the
# mapping to chromosome 6. However, I think we only get this mapping
# from our current source (NCBI seq_gene.md) anyway, so I'm not sure
# where we got the other mappings from in the past (but haven't
# investigated really).
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_000500.5:c.92C>T')
assert 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.
"""
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_001007553.1:c.*953delA' in coding
assert 'NM_001130523.1: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_002241.4: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 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 genomic == None
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert 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 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 genomic == None
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert 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 coding == None
erange = self.output.getMessagesWithErrorCode('ERANGE')
assert 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 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 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 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 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 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 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 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 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 len(erange) == 1
def test_ins_seq_chrom2c(self):
"""
Insertion of a sequence (chrom2c).
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000011.9:g.111957482_111957483insGAT', 'list')
assert 'NM_003002.2:c.-150_-149insGAT' in coding
assert 'NM_012459.2:c.10_11insATC' in coding
def test_ins_seq_seq(self):
"""
Insertion of two sequences (chrom2c).
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000011.9:g.111957482_111957483ins[GAT;AAA]', 'list')
assert 'NM_003002.2:c.-150_-149ins[GAT;AAA]' in coding
assert 'NM_012459.2:c.10_11ins[TTT;ATC]' in coding
def test_ins_seq_c2chrom_reverse(self):
"""
Insertion of a sequence on reverse strand (c2chrom).
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_012459.2:c.10_11insATC')
assert genomic == 'NC_000011.9:g.111957482_111957483insGAT'
def test_ins_seq_seq_c2chrom_reverse(self):
"""
Insertion of two sequences on reverse strand (c2chrom).
"""
converter = self._converter('hg19')
genomic = converter.c2chrom('NM_012459.2:c.10_11ins[TTT;ATC]')
assert genomic == 'NC_000011.9:g.111957482_111957483ins[GAT;AAA]'