def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling")
self.check_multi_files(
[self._args.fasta_files],
["--fasta_files"])
if (self._args.bam_type != "related_genome") and (
self._args.bam_type != "reference_genome"):
print("Error: Please assign \"related_genome\" or"
" \"reference_genome\" to --bam_type!")
sys.exit()
if (self._args.ploidy != "haploid") and (
self._args.ploidy != "diploid"):
print("Error: Please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!")
if (self._args.caller != "c") and (
self._args.caller != "m"):
print("Error: Please assign \"c\" or"
" \"m\" to --caller!")
for prop in ("bcftools_path", "samtools_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type,
self._args.program, self._args.fasta_files,
self._args.bam_files,
self._args.quality, self._args.read_depth_range,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy, self._args.rg_tag, self._args.caller,
self._args.filter_tag_info, self._args.dp4_cutoff)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(self.test_folder, "compare_reference"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs"))
os.mkdir(
os.path.join(self.test_folder,
"compare_reference/seqs/with_BAQ"))
os.mkdir(
os.path.join(self.test_folder, "compare_reference/statistics"))
args = self.mock_args.mock()
args.types = "reference"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling...")
self.check_folder([self._args.fasta_path])
if (self._args.bam_type != "target") and (
self._args.bam_type != "reference"):
print("Error: please assign \"target\" or"
" \"reference\" to --bam_type!!")
sys.exit()
if (self._args.ploidy != "haploid") and (
self._args.ploidy != "diploid"):
print("Error: please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!!")
if (self._args.caller != "c") and (
self._args.caller != "m"):
print("Error: please assign \"c\" or"
" \"m\" to --caller!!")
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type, self._args.sample_number,
self._args.program, self._args.fasta_path,
self._args.tex_bam_path, self._args.frag_bam_path,
self._args.quality, self._args.read_depth_range,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy, self._args.RG_tag, self._args.caller,
self._args.filter_tag_info, self._args.DP4_cutoff)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs"))
args = self.mock_args.mock()
args.types = "related_genome"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling...")
self.check_folder([self._args.fasta_path])
if (self._args.bam_type != "target") and (
self._args.bam_type != "reference"):
print("Error: please assign \"target\" or"
" \"reference\" to --bam_type!!")
sys.exit()
if (self._args.ploidy != "haploid") and (
self._args.ploidy != "diploid"):
print("Error: please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!!")
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type,
self._args.program, self._args.fasta_path,
self._args.tex_bam_path, self._args.frag_bam_path,
self._args.quality, self._args.read_depth,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
class TestSNPCalling(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(
os.path.join(self.test_folder,
"compare_related_and_reference_genomes"))
os.mkdir(
os.path.join(self.test_folder,
"compare_related_and_reference_genomes/seqs"))
os.mkdir(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ"))
os.mkdir(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics"))
os.mkdir(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs"))
args = self.mock_args.mock()
args.types = "related_genome"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp_folder = os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs/test")
os.mkdir(snp_folder)
snp = os.path.join(snp_folder, "test_with_BAQ_NC_007795.1.vcf")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
args.depth_s = "n_10"
args.depth_b = "a_2"
args.dp4_sum = "n_10"
args.dp4_frac = 0.5
args.idv = "n_10"
args.imf = 0.5
args.filters = ["VDB_s0.1"]
args.min_sample = 2
os.mkdir(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test"))
depth_file = os.path.join(self.test_folder, "tmp_depthNC_007795.1")
gen_file(depth_file, self.example.depth_file)
bam_datas = [{
"sample": "NC_007795.1",
"bam_number": 1,
"bams": "test",
"rep": 1
}]
self.snp._transcript_snp(
fasta,
"test",
"with",
"test",
bam_datas,
self.table,
args,
)
datas = import_data(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics/stat_test_with_BAQ_NC_007795.1_SNP_best.csv"
))
print("\n".join(datas))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test/test_NC_007795.1_NC_007795.1_1_1.fa"
))
self.assertEqual("\n".join(datas),
">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_NC_007795.1_seq_reference.csv")
os.remove("test_NC_007795.1_best.vcf")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_best.png")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_raw.png")
def test_run_program(self):
self.snp._run_sub = self.mock.mock_run_sub
args = self.mock_args.mock()
bam_datas = [{
"sample": "NC_007795.1",
"bam_number": 1,
"bams": "test",
"rep": 1
}]
args.program = ["with_BAQ"]
self.snp._run_program("fasta", bam_datas, args)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test")))
def test_merge_bams(self):
args = self.mock_args.mock()
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
bam_datas = [{
"sample": "NC_007795.1",
"bam_number": 0,
"bams": "test",
"rep": 1
}]
self.snp._run_bam = self.mock.mock_run_bam
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.bams = [args.frag_bams, args.normal_bams]
args.samtools_path = "test"
self.snp._merge_bams(args, bam_datas)
self.assertEqual(bam_datas[0]["bam_number"], 1)
def test_modify_header(self):
gen_file(os.path.join(self.fasta, "test.fa"),
">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
self.snp._modify_header(self.fasta)
datas = import_data(os.path.join(self.fasta, "test.fa"))
self.assertEqual("\n".join(datas), ">DDD\nAATTAATTGGCC")
def test_get_genome_name(self):
self.snp._get_header = self.mock.mock_get_header
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
args = self.mock_args.mock()
args.samtools_path = "test"
bam_datas = [{
"sample": "NC_007795.1",
"bam_number": 0,
"bams": "test",
"rep": 1
}]
seq_names = self.snp._get_genome_name(args, bam_datas)
def test_run_snp_calling(self):
self.snp._get_header = self.mock.mock_get_header
self.snp._run_bam = self.mock.mock_run_bam
self.snp._run_sub = self.mock.mock_run_sub
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
gen_file(os.path.join(self.fasta, "test.fa"),
">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
gen_file(os.path.join(self.test_folder, "whole_reads.bam"), "test")
gen_file(os.path.join(self.test_folder, "whole_reads_sorted.bam"),
"test")
gen_file(os.path.join(self.test_folder, "tmp_bcf"), "test")
gen_file(os.path.join(self.fasta, "all.fa.fai"), "test")
args = self.mock_args.mock()
args.types = "reference"
args.program = ["with_BAQ"]
args.bams = [
"a1:" + os.path.join(self.test_folder, "frag_bams"),
"a2:" + os.path.join(self.test_folder, "tex_bams")
]
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
self.snp.run_snp_calling(args)
class TestSNPCalling(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics"))
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs"))
args = self.mock_args.mock()
args.types = "related_genome"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp_folder = os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs/test")
os.mkdir(snp_folder)
snp = os.path.join(snp_folder, "test_with_BAQ_NC_007795.1.vcf")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
args.depth_s = "n_10"
args.depth_b = "a_2"
args.dp4_sum = "n_10"
args.dp4_frac = 0.5
args.idv = "n_10"
args.imf = 0.5
args.filters = ["VDB_s0.1"]
args.min_sample = 2
os.mkdir(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test"))
depth_file = os.path.join(self.test_folder, "tmp_depthNC_007795.1")
gen_file(depth_file, self.example.depth_file)
bam_datas = [{"sample": "NC_007795.1", "bam_number": 1,
"bams": "test", "rep": 1}]
self.snp._transcript_snp(fasta, "test", "with",
"test", bam_datas, self.table, args,)
datas = import_data(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics/stat_test_with_BAQ_NC_007795.1_SNP_best.csv"))
print("\n".join(datas))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test/test_NC_007795.1_NC_007795.1_1_1.fa"))
self.assertEqual("\n".join(datas),
">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_NC_007795.1_seq_reference.csv")
os.remove("test_NC_007795.1_best.vcf")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_best.png")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_raw.png")
def test_run_program(self):
self.snp._run_sub = self.mock.mock_run_sub
args = self.mock_args.mock()
bam_datas = [{"sample": "NC_007795.1", "bam_number": 1,
"bams": "test", "rep": 1}]
args.program = ["with_BAQ"]
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.snp._run_program("fasta", bam_datas, args, log)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test")))
def test_merge_bams(self):
args = self.mock_args.mock()
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
bam_datas = [{"sample": "NC_007795.1", "bam_number": 0,
"bams": "test", "rep": 1}]
self.snp._run_bam = self.mock.mock_run_bam
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.bams = [args.frag_bams, args.normal_bams]
args.samtools_path = "test"
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.snp._merge_bams(args, bam_datas, log)
self.assertEqual(bam_datas[0]["bam_number"], 1)
def test_modify_header(self):
gen_file(os.path.join(self.fasta, "test.fa"),
">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
self.snp._modify_header(self.fasta)
datas = import_data(os.path.join(self.fasta, "test.fa"))
self.assertEqual("\n".join(datas), ">DDD\nAATTAATTGGCC")
def test_get_genome_name(self):
self.snp._get_header = self.mock.mock_get_header
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
args = self.mock_args.mock()
args.samtools_path = "test"
bam_datas = [{"sample": "NC_007795.1", "bam_number": 0,
"bams": "test", "rep": 1}]
seq_names = self.snp._get_genome_name(args, bam_datas)
def test_run_snp_calling(self):
self.snp._get_header = self.mock.mock_get_header
self.snp._run_bam = self.mock.mock_run_bam
self.snp._run_sub = self.mock.mock_run_sub
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
gen_file(os.path.join(self.fasta, "test.fa"),
">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
gen_file(os.path.join(self.test_folder, "whole_reads.bam"), "test")
gen_file(os.path.join(self.test_folder, "whole_reads_sorted.bam"),
"test")
gen_file(os.path.join(self.test_folder, "tmp_bcf"), "test")
gen_file(os.path.join(self.fasta, "all.fa.fai"), "test")
args = self.mock_args.mock()
args.types = "reference"
args.program = ["with_BAQ"]
args.bams = ["a1:" + os.path.join(self.test_folder, "frag_bams"),
"a2:" + os.path.join(self.test_folder, "tex_bams")]
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.snp.run_snp_calling(args, log)
class TestSNPCalling(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(self.test_folder, "compare_reference"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/statistics"))
args = self.mock_args.mock()
args.types = "reference"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_import_bam(self):
gen_file(os.path.join(self.test_folder, "test_1.bam"), "test")
gen_file(os.path.join(self.test_folder, "test_2.bam"), "test")
bams = []
num_bams = self.snp._import_bam(self.test_folder, bams)
self.assertEqual(num_bams, 2)
self.assertListEqual(bams, ['test_folder/test_1.bam', 'test_folder/test_2.bam'])
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp = os.path.join(self.test_folder, "NC_007795.1.csv")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test"))
self.snp._transcript_snp(fasta, snp, "test", "with",
"test", 10, self.table, args)
datas = import_data(os.path.join(self.test_folder, "compare_reference/statistics/stat_test_with_BAQ_SNP.csv"))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test/test_NC_007795.1_1_1.fa"))
self.assertEqual("\n".join(datas), ">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_seq_reference.csv")
os.remove("test_depth_only.vcf")
os.remove("test_depth_quality.vcf")
os.remove("test_NC_007795.1_SNP_QUAL.png")
def test_run_sub(self):
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
file_prefixs = {"raw_prefix": "test",
"table_prefix": "test"}
args = self.mock_args.mock()
self.snp._run_sub(args, "fasta", "with", file_prefixs, "test",
self.test_folder, 10)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test")))
def test_run_program(self):
self.snp._run_sub = self.mock.mock_run_sub
args = self.mock_args.mock()
args.program = ["1"]
self.snp._run_program("fasta", "test", "test", 10,
"table", args)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test")))
def test_detect_fasta(self):
datas = self.snp._detect_fasta("test.fa")
self.assertEqual(datas, (True, 'test'))
def test_merge_bams(self):
args = self.mock_args.mock()
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
self.snp._run_bam = self.mock.mock_run_bam
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
num = self.snp._merge_bams(args)
self.assertEqual(num, 3)
def test_modify_header(self):
gen_file(os.path.join(self.fasta, "test.fa"), ">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
self.snp._modify_header(self.fasta)
datas = import_data(os.path.join(self.fasta, "test.fa"))
self.assertEqual("\n".join(datas), ">DDD\nAATTAATTGGCC")
def test_get_genome_name(self):
self.snp._get_header = self.mock.mock_get_header
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
seq_names = self.snp._get_genome_name("test")
def test_run_snp_calling(self):
self.snp._get_header = self.mock.mock_get_header
self.snp._run_bam = self.mock.mock_run_bam
self.snp._run_sub = self.mock.mock_run_sub
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
gen_file(os.path.join(self.fasta, "test.fa"), ">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
gen_file(os.path.join(self.test_folder, "whole_reads.bam"), "test")
gen_file(os.path.join(self.test_folder, "whole_reads_sorted.bam"), "test")
args = self.mock_args.mock()
args.types = "reference"
args.program = ["1"]
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
self.snp.run_snp_calling(args)
class TestSNPCalling(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.fasta = os.path.join(self.test_folder, "fasta")
self.snp_folder = os.path.join(self.test_folder, "snp")
self.table = os.path.join(self.test_folder, "table")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.fasta)
os.mkdir(self.snp_folder)
os.mkdir(self.table)
os.mkdir(os.path.join(self.test_folder, "compare_reference"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ"))
os.mkdir(os.path.join(self.test_folder, "compare_reference/statistics"))
args = self.mock_args.mock()
args.types = "reference"
args.out_folder = self.test_folder
args.fastas = self.fasta
self.snp = SNPCalling(args)
self.mock = Mock_func()
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_import_bam(self):
gen_file(os.path.join(self.test_folder, "test_1.bam"), "test")
gen_file(os.path.join(self.test_folder, "test_2.bam"), "test")
bams = []
num_bams = self.snp._import_bam(self.test_folder, bams)
self.assertEqual(num_bams, 2)
self.assertListEqual(bams, ['test_folder/test_1.bam', 'test_folder/test_2.bam'])
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp = os.path.join(self.test_folder, "NC_007795.1.csv")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
args.depth_s = "n_10"
args.depth_b = "a_2"
args.dp4_sum = "n_10"
args.dp4_frac = 0.5
args.idv = "n_10"
args.imf = 0.5
args.filters = ["VDB_s0.1"]
args.min_sample = 2
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test"))
depth_file = os.path.join(self.test_folder, "tmp_depth")
gen_file(depth_file, self.example.depth_file)
self.snp._transcript_snp(fasta, snp, "test", "with",
"test", 10, self.table, args)
datas = import_data(os.path.join(self.test_folder, "compare_reference/statistics/stat_test_with_BAQ_SNP_best.csv"))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test/test_NC_007795.1_1_1.fa"))
self.assertEqual("\n".join(datas), ">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_seq_reference.csv")
os.remove("test_best.vcf")
os.remove("test_NC_007795.1_SNP_QUAL_best.png")
os.remove("test_NC_007795.1_SNP_QUAL_raw.png")
def test_run_sub(self):
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
file_prefixs = {"raw_prefix": "test",
"table_prefix": "test"}
args = self.mock_args.mock()
self.snp._run_sub(args, "fasta", "with", file_prefixs, "test",
self.test_folder, 10)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test")))
def test_run_program(self):
self.snp._run_sub = self.mock.mock_run_sub
args = self.mock_args.mock()
args.program = ["1"]
self.snp._run_program("fasta", "test", "test", 10,
"table", args)
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test")))
def test_detect_fasta(self):
datas = self.snp._detect_fasta("test.fa")
self.assertEqual(datas, (True, 'test'))
def test_merge_bams(self):
args = self.mock_args.mock()
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
self.snp._run_bam = self.mock.mock_run_bam
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
num = self.snp._merge_bams(args)
self.assertEqual(num, 3)
def test_modify_header(self):
gen_file(os.path.join(self.fasta, "test.fa"), ">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
self.snp._modify_header(self.fasta)
datas = import_data(os.path.join(self.fasta, "test.fa"))
self.assertEqual("\n".join(datas), ">DDD\nAATTAATTGGCC")
def test_get_genome_name(self):
self.snp._get_header = self.mock.mock_get_header
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
args = self.mock_args.mock()
args.samtools_path = "test"
seq_names = self.snp._get_genome_name(args)
def test_run_snp_calling(self):
self.snp._get_header = self.mock.mock_get_header
self.snp._run_bam = self.mock.mock_run_bam
self.snp._run_sub = self.mock.mock_run_sub
self.snp._run_tools = self.mock.mock_run_tools
self.snp._transcript_snp = self.mock.mock_transcript_snp
gen_file(os.path.join(self.fasta, "test.fa"), ">AAA|BBB|CCC|DDD|EEE\nAATTAATTGGCC")
gen_file(os.path.join(self.test_folder, "header"), self.example.bam)
gen_file(os.path.join(self.test_folder, "whole_reads.bam"), "test")
gen_file(os.path.join(self.test_folder, "whole_reads_sorted.bam"), "test")
args = self.mock_args.mock()
args.types = "reference"
args.program = ["1"]
args.frag_bams = os.path.join(self.test_folder, "frag_bams")
args.normal_bams = os.path.join(self.test_folder, "tex_bams")
os.mkdir(args.normal_bams)
os.mkdir(args.frag_bams)
gen_file(os.path.join(args.normal_bams, "tex.bam"), "test")
gen_file(os.path.join(args.normal_bams, "notex.bam"), "test")
gen_file(os.path.join(args.frag_bams, "farg.bam"), "test")
args.samtools_path = "test"
self.snp.run_snp_calling(args)