def test_bowtie2_exec_notexist():
"""Error thrown if bowtie2 executable does not exist"""
try:
obj = bowtie_map.Bowtie2_Map(os.path.join(".", "bowtie2"))
except NotExecutableError:
return True
else:
return False
def test_bowtie2_notexec():
"""Error thrown if bowtie2 not executable"""
try:
obj = bowtie_map.Bowtie2_Map("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_bowtie2_cmd():
"""bowtie2-map returns correct form of cmd-line"""
bt2_map = bowtie_map.Bowtie2_Map("bowtie2")
outfilename = os.path.join(OUTDIR,
"_vs_".join([os.path.split(os.path.splitext(READS)[0])[-1],
os.path.split(os.path.splitext(FA_INDEX)[0])[-1]]) + ".sam")
target = ' '.join(["bowtie2",
"--very-sensitive",
"--no-unal",
"-p", THREADS,
"-x", FA_INDEX,
"-f", READS,
"-S", outfilename])
result = bt2_map.run(READS.split(".gz")[0], FA_INDEX,
outfilename, THREADS, fasta=True, dry_run=True)
assert_equal(result.command, target)
def test_bowtie2_build_exec():
"""bowtie2 maps reads correctly with FASTA test data"""
bt2_map = bowtie_map.Bowtie2_Map("bowtie2")
outfilename = os.path.join(OUTDIR,
"_vs_".join([os.path.split(os.path.splitext(READS)[0])[-1],
os.path.split(os.path.splitext(FA_INDEX)[0])[-1]]) +
".sam")
result = bt2_map.run(READS, FA_INDEX, outfilename, THREADS, fasta=True)
# Test for equality of output and target MD5 files
# To establish equality, we need to ignore the @PG line that describes the
# path to bowtie2, as this may differ between systems
with open(os.path.join(outfilename), "r") as outfh:
with open(TARGET, "r") as tgtfh:
tgtdata = '\n'.join([l for l in tgtfh.readlines() if
not l.startswith('@PG')])
outdata = '\n'.join([l for l in outfh.readlines() if
not l.startswith('@PG')])
assert_equal(tgtdata, outdata)
def test_bowtie_map_cmd_fq():
"""bowtie2 map instantiates FQ input, runs and returns correct
form of cmd-line"""
obj = bowtie_map.Bowtie2_Map("bowtie2")
first = os.path.split(ASSEM_READS)[-1].split(".f")[0]
second = "_Vs_" + os.path.split(FA_INDEX)[-1] + ".sam"
outfile_name = first + second
target = ' '.join(["bowtie2",
"--very-sensitive",
"--no-unal",
"-p", THREADS,
"-x",
FA_INDEX,
"-q",
ASSEM_READS,
"-S",
os.path.join(OUTDIR, outfile_name)])
assert_equal(obj.run(ASSEM_READS, FA_INDEX, OUTDIR, THREADS,
dry_run=True),
target)
def test_bowtie_map_FQ_exec():
"""Run bowtie_map on test FQ data and compare output
to precomputed target"""
# wont work with .gz files, so have to decomp these
decompcmd = decomp(ASSEM_READS)
pipe = subprocess.run(decompcmd, shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True)
obj = bowtie_map.Bowtie2_Map("bowtie2")
result = obj.run(ASSEM_READS.split(".gz")[0], FA_INDEX,
OUTDIR, THREADS)
# compress them again
comp_cmd = comp(ASSEM_READS.split(".gz")[0])
pipe = subprocess.run(comp_cmd, shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True)
# test to see if it has produced the sam file.
if not os.path.isfile(result.sam):
return False
def test_bowtie2path():
"""bowtie2-map executable is in $PATH"""
bowtie_map.Bowtie2_Map("bowtie2")
def test_bowtie():
"""bowtie_map instantiates with cmd-line if bowtie is in $PATH"""
bowtie_map.Bowtie2_Map("bowtie2")