def test_hisat(self):
"""Test hisat index creation, FaQC, and mapping."""
dir_path = os.path.dirname(os.path.realpath(__file__))
bindir = os.path.abspath(os.path.join(dir_path, '..', 'bin'))
luigi.interface.build([
Map.HisatIndex(fasta="tests/data/test_prok.fna",
hi_index="tests/test_hisatmapping/prok_index",
num_cpus=1),
Map.Hisat(fastqs=[
"tests/data/BTT_test15_R1.1000.fastq",
"tests/data/BTT_test15_R2.1000.fastq"
],
num_cpus=1,
sample="samp1",
faqc_min_L=50,
n_cutoff=5,
qc_outdir="tests/test_hisatmapping/trimming_results",
map_dir="tests/test_hisatmapping/mapping_results",
indexfile="tests/test_hisatmapping/prok_index",
spliceFile="",
outsam="tests/test_hisatmapping/samp1.sam",
ref_file="tests/data/test_prok.fa",
workdir="tests/test_hisatmapping/")
],
local_scheduler=True)
self.assertTrue(
os.path.exists("tests/test_hisatmapping/prok_index.8.ht2l"))
self.assertTrue(os.path.exists("tests/test_hisatmapping/samp1.sam"))
def test_hisat(self):
"""Test hisat index creation, FastQC, and mapping."""
luigi.interface.build([
Map.HisatIndex(fasta="tests/data/test_prok.fa",
hi_index="tests/test_hisatmapping/prok_index",
bindir="bin",
numCPUs=1),
FastQC.PairedRunQC(
fastqs=[
"tests/data/BTT_test15_R1.1000.fastq",
"tests/data/BTT_test15_R2.1000.fastq"
],
sample="samp1",
numCPUs=1,
outdir="tests/test_hisatmapping/trimming_results",
bindir="bin"),
Map.Hisat(fastq1="tests/data/BTT_test15_R1.1000.fastq",
fastq2="tests/data/BTT_test15_R2.1000.fastq",
numCPUs=1,
indexfile="tests/test_hisatmapping/prok_index",
spliceFile="",
mappingLogFile="tests/test_hisatmapping/mapping.log",
unalned="tests/test_hisatmapping//unligned.fastq",
outsam="tests/test_hisatmapping/samp1.sam",
ref_file="tests/data/test_prok.fa",
bindir="bin")
],
local_scheduler=True)
self.assertTrue(
os.path.exists("tests/test_hisatmapping/prok_index.8.ht2l"))
self.assertTrue(os.path.exists("tests/test_hisatmapping/samp1.sam"))
def test_splice_creation(self):
"""Test if CreateSplice works."""
luigi.interface.build([
Map.GFF2GTF(gff_file="tests/data/test_prok.gff",
workdir="tests/test_createsplice"),
Map.CreateSplice(gff_file="tests/data/test_prok.gff",
workdir="tests/test_createsplice")
],
local_scheduler=True)
self.assertTrue(
os.path.exists("tests/test_createsplice/test_prok.splice"))
def test_splices_creation(self):
"""Test if GFF2GTF works for multiple gffs."""
luigi.interface.build([
Map.GFF2GTF(
gff_file=
"tests/data/test_prok1.1.gff,tests/data/eukarya_test.gff3",
workdir="tests/test_createsplice"),
Map.CreateSplice(
gff_file=
"tests/data/test_prok1.1.gff,tests/data/eukarya_test.gff3",
workdir="tests/test_createsplice")
],
local_scheduler=True)
self.assertTrue(
os.path.exists("tests/test_createsplice/test_prok1.1.splice"))
self.assertTrue(
os.path.exists("tests/test_createsplice/eukarya_test.splice"))
def test_gtf_creation(self):
"""Test if GFF2GTF works."""
luigi.interface.build([
Map.GFF2GTF(gff_file="tests/data/test_prok.gff",
workdir="tests/test_gff2gtf")
],
local_scheduler=True)
self.assertTrue(os.path.exists("tests/test_gff2gtf/test_prok.gtf"))
def test_splices_creation(self):
"""Test if GFF2GTF works for multiple gffs."""
luigi.interface.build([
Map.GFF2GTF(
gff_file=
"tests/data/test_prok1.1.gff,tests/data/eukarya_test.gff3",
bindir="bin",
workdir="tests/test_createsplice"),
Map.CreateSplice(
gff_file=
"tests/data/test_prok1.1.gff,tests/data/eukarya_test.gff3",
bindir="bin",
workdir="tests/test_createsplice")
],
local_scheduler=True)
self.assertTrue(
os.path.exists("tests/test_createsplice/test_prok1.1.splice"))
self.assertTrue(
os.path.exists("tests/test_createsplice/eukarya_test.splice"))
with open("tests/test_createsplice/eukarya_test.splice") as pg:
first_line_second_column = pg.readline().split("\t")[1]
self.assertEqual(first_line_second_column, "220")
def test_star():
"""Test star index creation, FaQC, and mapping."""
luigi.interface.build([Map.star(fastqs=["tests/data/BTT_test15_R1.1000.fastq",
"tests/data/BTT_test15_R2.1000.fastq"],
num_cpus=1,
fasta="tests/data2/chr22_ERCC92.fa",
stardb_dir="tests/test_star_mapping/index",
map_dir="tests/test_star_mapping/mapping_results",
gff_file="tests/data2/chr22_ERCC92.gff3",
sample="migun")], local_scheduler=True)
assert os.path.exists("tests/test_star_mapping/mapping_results/migun_Aligned.sortedByCoord.out.bam") is True
rm_cmd = rm["-rf", "tests/test_star_mapping"]
rm_cmd()
def test_gtfs_creation(self):
"""Test if GFF2GTF works for multiple gffs."""
luigi.interface.build([
Map.GFF2GTF(
gff_file=
"tests/data/test_prok.gff,tests/data/eukarya_test.gff3",
workdir="tests/test_gff2gtf")
],
local_scheduler=True)
self.assertTrue(os.path.exists("tests/test_gff2gtf/test_prok.gtf"))
self.assertTrue(os.path.exists("tests/test_gff2gtf/eukarya_test.gtf"))
with open("tests/test_gff2gtf/test_prok.gtf") as pg:
lines = pg.readlines()
self.assertEqual(lines[5].split("\t")[4], "1747")
with open("tests/test_gff2gtf/eukarya_test.gtf") as pg:
lines = pg.readlines()
self.assertEqual(lines[5].split("\t")[4], "3007")
def test_gtfs_creation(self):
"""Test if GFF2GTF works for multiple gffs."""
luigi.interface.build([
Map.GFF2GTF(
gff_file=
"tests/data/test_prok.gff,tests/data/eukarya_test.gff3",
bindir="bin",
workdir="tests/test_gff2gtf")
],
local_scheduler=True)
self.assertTrue(os.path.exists("tests/test_gff2gtf/test_prok.gtf"))
self.assertTrue(os.path.exists("tests/test_gff2gtf/eukarya_test.gtf"))
with open("tests/test_gff2gtf/test_prok.gtf") as pg:
first_line_fourth_column = pg.readline().split("\t")[3]
self.assertEqual(first_line_fourth_column, "462")
with open("tests/test_gff2gtf/eukarya_test.gtf") as pg:
first_line_fifth_column = pg.readline().split("\t")[4]
self.assertEqual(first_line_fifth_column, "2754")