def create_interfaces(args, logger):
"""Check third-party executable dependencies exist and instantiate.
The instantiated interfaces are returned.
"""
# Check for presence of third-party tools, by instantiating interfaces
logger.info("Checking third-party packages:")
logger.info("\tFastQC... (%s)", args.fastqc)
fastqc_qc = fastqc.FastQC(args.fastqc)
logger.info("\ttrim_quality... (%s)", args.trim_quality)
trim_quality = seq_crumbs.Trim_Quality(args.trim_quality, logger)
logger.info("\tjoin_paired_ends.py... (%s)", args.join_paired_ends)
jpe = qiime.Join_Paired_Ends(args.join_paired_ends, logger)
logger.info("\tconvert_format... (%s)", args.convert_format)
convert_format = seq_crumbs.Convert_Format(args.convert_format, logger)
logger.info("\tblastclust... (%s)", args.blastclust)
blastclust = blast.Blastclust(args.blastclust)
logger.info("\tmuscle... (%s)", args.muscle)
muscle_aln = muscle.Muscle(args.muscle)
logger.info("\tpick_otus.py... (%s)", args.pick_otus)
pick_otus = qiime.Pick_Otus(args.pick_otus, logger)
logger.info("\tpick_closed_reference_otus.py... (%s)",
args.pick_closed_reference_otus)
pcro = qiime.Pick_Closed_Ref_Otus(args.pick_closed_reference_otus, logger)
return (fastqc_qc, trim_quality, jpe, convert_format, blastclust,
muscle_aln, pick_otus, pcro)
def test_blastclust_exec():
"""Run blastclust on test data and compare output to precomputed target"""
bc = blast.Blastclust("blastclust")
result = bc.run(os.path.join(INDIR, "trimmed.fasta"), OUTDIR, THREADS)
with open(TARGET, "r") as target_fh:
with open(result.outfilename, "r") as test_fh:
assert_equal(target_fh.read(), test_fh.read())
def test_blastclust_notexec():
"""Error thrown if blastclust exe not executable"""
try:
bc = blast.Blastclust("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_blastclust_exec_notexist():
"""Error thrown if executable does not exist"""
try:
bc = blast.Blastclust(os.path.join(".", "blastclust"))
except NotExecutableError:
return True
else:
return False
def test_blastclust_cmd():
"""Blastclust instantiates and returns correct form of cmd-line"""
bc = blast.Blastclust("blastclust")
target = ' '.join(["blastclust -L 0.90 -S 99 -a 4 -p F",
"-i trimmed.fasta",
"-o",
os.path.join("test_out",
"trimmed.fasta.blastclust99.lst")])
assert_equal(bc.run("trimmed.fasta", "test_out", 4, dry_run=True),
target)
def test_blastclust_cmd():
"""Blastclust instantiates and returns correct form of cmd-line"""
bc = blast.Blastclust("blastclust")
target = ' '.join([
"blastclust", "-L 0.90", "-S 99", "-a 4", "-p F", "-i trimmed.fasta",
"-o",
os.path.join("tests", "test_out", "blastclust",
"trimmed.fasta.blastclust99.lst")
])
result = bc.run("trimmed.fasta", OUTDIR, 4, dry_run=True)
assert_equal(result.command, target)
def test_blastclust_exec():
"""Run blastclust on test data and compare output to precomputed target"""
bc = blast.Blastclust("blastclust")
try:
shutil.rmtree(OUTDIR)
except FileNotFoundError:
pass
os.makedirs(OUTDIR, exist_ok=True)
result = bc.run(os.path.join(INDIR, "trimmed.fasta"), OUTDIR, THREADS)
with open(TARGET, "r") as target_fh:
with open(result.outfilename, "r") as test_fh:
assert_equal(target_fh.read(), test_fh.read())
def test_blastclust():
"""Blastclust instantiates with cmd-line and blastclust is in $PATH"""
blast.Blastclust("blastclust")
"'%s' contains whitespace" % fname)
logger.error("(exiting)")
sys.exit(1)
# Check for presence of third-party tools, by instantiating interfaces
logger.info("Checking third-party packages:")
logger.info("\tFastQC... (%s)" % args.fastqc)
fastQC = fastqc.FastQC(args.fastqc, logger)
logger.info("\ttrim_quality... (%s)" % args.trim_quality)
trim_quality = seq_crumbs.Trim_Quality(args.trim_quality, logger)
logger.info("\tjoin_paired_ends.py... (%s)" % args.join_paired_ends)
jpe = qiime.Join_Paired_Ends(args.join_paired_ends, logger)
logger.info("\tconvert_format... (%s)" % args.convert_format)
convert_format = seq_crumbs.Convert_Format(args.convert_format, logger)
logger.info("\tblastclust... (%s)" % args.blastclust)
blastclust = blast.Blastclust(args.blastclust)
logger.info("\tmuscle... (%s)" % args.muscle)
muscle = muscle.Muscle(args.muscle, logger)
logger.info("\tpick_otus.py... (%s)" % args.pick_otus)
pick_otus = qiime.Pick_Otus(args.pick_otus, logger)
logger.info("\tpick_closed_reference_otus.py... (%s)" %
args.pick_closed_reference_otus)
pcro = qiime.Pick_Closed_Ref_Otus(args.pick_closed_reference_otus, logger)
# How many threads are we using?
args.threads = min(args.threads, multiprocessing.cpu_count())
logger.info("Using %d threads/CPUs where available" % args.threads)
# Trim reads on quality - forward and reverse reads
logger.info("Trim reads by quality")
try:
def test_blastclust():
"""blastclust is in $PATH"""
blast.Blastclust("blastclust")