def test_vphaser_one_sample(self):
# Files here were created as follows:
# - in.bam was copied from input directory for TestVPhaser2; see notes
# there on how it was created.
# - ref.fasta was created by making two identical chromosomes, chr1
# and chr2, with the sequence from West Nile virus isolate
# WNV-1/US/BID-V7821/2011. That genome is a guess for the reference
# of the V-Phaser 2 test file because BLAST matches the reads to
# West Nile virus and that isolate has the size reported in the bam file.
# Note that ref.fasta is not exactly the consensus of the reads in in.bam;
# for example, pos 660 is C in ref.fasta, but more reads have T there
# than C in in.bam. So we are actually testing the case that
# V-Phaser 2 consensus != our consensus.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam,
refFasta,
outTab,
vphaserNumThreads=4,
minReadsEach=6,
maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_2libs(self):
# in.2libs.bam was created by "manually" editing in.bam and moving about
# 1/3 of the reads to ReadGroup2.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.2libs.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=6, maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_2libs_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_2libs(self):
# in.2libs.bam was created by "manually" editing in.bam and moving about
# 1/3 of the reads to ReadGroup2.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.2libs.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=6, maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_2libs_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_one_mate_unpaired(self):
# Files here were created as follows:
# ref.indels.fasta is Seed-stock-137_S2_L001_001.fasta
# in.oneunmapped.bam was created from in.indels.bam, with flag 0->89, 16->73:
# When removing doubly mapped reads, doing so can result in all reads
# being removed in the case of low-quality runs with few reads
# This tests that when v-phaser2 input is empty, a blank
# file is created as output.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.oneunmapped.bam')
refFasta = os.path.join(myInputDir, 'ref.indels.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=0, removeDoublyMappedReads=True)
assert os.path.getsize(outTab) == 0
def test_vphaser_one_sample_3libs_and_chi2(self):
# In addition to testing that we can handle 3 libraries, this is testing
# the chi2_contingency approximation to fisher_exact. The 4th, 5th,
# and 6th rows have large enough minor allele count that their
# p-values are calculated using the chi2 approximation. The other
# rows are testing the 2 x 3 case of fisher_exact.
# in.3libs.bam was created by "manually" editing in.2libs.bam and moving
# about 1/2 of the reads in ReadGroup2 to ReadGroup3.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.3libs.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=6, maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_3libs_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_3libs_and_chi2(self):
# In addition to testing that we can handle 3 libraries, this is testing
# the chi2_contingency approximation to fisher_exact. The 4th, 5th,
# and 6th rows have large enough minor allele count that their
# p-values are calculated using the chi2 approximation. The other
# rows are testing the 2 x 3 case of fisher_exact.
# in.3libs.bam was created by "manually" editing in.2libs.bam and moving
# about 1/2 of the reads in ReadGroup2 to ReadGroup3.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.3libs.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=6, maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_3libs_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_indels(self):
# Files here were created as follows:
# ref.indels.fasta is Seed-stock-137_S2_L001_001.fasta
# in.indels.bam was created from Seed-stock-137_S2_L001_001.mapped.bam
# as follows:
# Created two .sam files using samtools view, restricting to ranges
# 6811-7011 and 13081-13281, respectively. Paired reads were removed
# from those files by throwing out the second occurence of any read name
# and anding the flag fields with 16. Then, a random 90% of reads were
# removed, except that any reads containing the indel variants at
# 6911 and 13181 were kept. Then the resulting 2 files were combined.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.indels.bam')
refFasta = os.path.join(myInputDir, 'ref.indels.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=0)
expected = os.path.join(myInputDir, 'vphaser_one_sample_indels_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample_indels(self):
# Files here were created as follows:
# ref.indels.fasta is Seed-stock-137_S2_L001_001.fasta
# in.indels.bam was created from Seed-stock-137_S2_L001_001.mapped.bam
# as follows:
# Created two .sam files using samtools view, restricting to ranges
# 6811-7011 and 13081-13281, respectively. Paired reads were removed
# from those files by throwing out the second occurence of any read name
# and anding the flag fields with 16. Then, a random 90% of reads were
# removed, except that any reads containing the indel variants at
# 6911 and 13181 were kept. Then the resulting 2 files were combined.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.indels.bam')
refFasta = os.path.join(myInputDir, 'ref.indels.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=0)
expected = os.path.join(myInputDir, 'vphaser_one_sample_indels_expected.txt')
self.assertEqualContents(outTab, expected)
def test_vphaser_one_sample(self):
# Files here were created as follows:
# - in.bam was copied from input directory for TestVPhaser2; see notes
# there on how it was created.
# - ref.fasta was created by making two identical chromosomes, chr1
# and chr2, with the sequence from West Nile virus isolate
# WNV-1/US/BID-V7821/2011. That genome is a guess for the reference
# of the V-Phaser 2 test file because BLAST matches the reads to
# West Nile virus and that isolate has the size reported in the bam file.
# Note that ref.fasta is not exactly the consensus of the reads in in.bam;
# for example, pos 660 is C in ref.fasta, but more reads have T there
# than C in in.bam. So we are actually testing the case that
# V-Phaser 2 consensus != our consensus.
myInputDir = util.file.get_test_input_path(self)
inBam = os.path.join(myInputDir, 'in.bam')
refFasta = os.path.join(myInputDir, 'ref.fasta')
outTab = util.file.mkstempfname('.txt')
intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=4, minReadsEach=6, maxBias=3)
expected = os.path.join(myInputDir, 'vphaser_one_sample_expected.txt')
self.assertEqualContents(outTab, expected)
