def test_muscle_exec():
"""muscle aligns test data"""
muscle_aln = muscle.Muscle("muscle")
result = muscle_aln.run(INFILE, OUTFILE)
with open(TARGET, "r") as target_fh:
with open(result.outfile, "r") as test_fh:
assert_equal(target_fh.read(), test_fh.read())
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_muscle_cmd():
"""muscle instantiates, runs and returns correct form of cmd-line"""
obj = muscle.Muscle("muscle")
target = ' '.join(
["muscle", "-in", FASTA, "-out", (os.path.join(OUTFOLDER, OUTFILE))])
qc = obj.run(FASTA, OUTFILE, OUTFOLDER)
assert_equal(qc.command, target)
def test_muscle_notexec():
"""Error thrown if muscle exe not executable"""
try:
obj = muscle.Muscle("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_muscle_exec_notexist():
"""Error thrown if muscle executable does not exist"""
try:
obj = muscle.Muscle(os.path.join(".", "muscle"))
except NotExecutableError:
return True
else:
return False
def test_muscle_exec():
"""Run muscle on test data and compare output to precomputed target"""
obj = muscle.Muscle("muscle")
try:
shutil.rmtree(OUTFILE)
except FileNotFoundError:
pass
os.makedirs(OUTFILE, exist_ok=True)
result = obj.run(FASTA, OUTFILE, OUTFOLDER)
with open(TARGET, "r") as target_fh:
with open(result.muscle_outfile, "r") as test_fh:
assert_equal(target_fh.read(), test_fh.read())
def check_tools_exist(WARNINGS):
"""function to check to see what tools are in the PATH,
decide what we can use
Returns a list of programs that were exectable and a warning string.
The warnings are tools that were not executable"""
tools_list = []
Warning_out = WARNINGS + "Tool executable warning: "
try:
trimmomatic.Trimmomatic(args.trimmomatic)
tools_list.append("trimmomatic")
except ValueError:
Warning_out = Warning_out + "trimmomatic not in path\n"
try:
muscle.Muscle(args.muscle)
tools_list.append("muscle")
except ValueError:
Warning_out = Warning_out + "muscle not in path\n"
return tools_list, Warning_out
def test_muscle():
"""muscle instantiates with cmd-line if muscle is in $PATH"""
muscle.Muscle("muscle")
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:
trimmed_fnames = [
trim_quality.run(fname, args.outdirname) for fname in infilenames
def test_muscle_cmd():
"""muscle wrapper returns correct form of cmd-line"""
muscle_aln = muscle.Muscle("muscle")
muscle_result = muscle_aln.run(INFILE, OUTFILE, dry_run=True)
target = ' '.join(['muscle', '-in', INFILE, '-out', OUTFILE])
assert_equal(muscle_result.command, target)
def test_muscle_path():
"""muscle executable is in $PATH"""
muscle_aln = muscle.Muscle("muscle")