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_fastqc_cmd():
"""fastqc instantiates, runs and returns correct form of cmd-line"""
obj = fastqc.FastQC("fastqc")
target = ' '.join(["fastqc", READS1, "-o", OUTDIR])
qc = obj.run(READS1, OUTDIR)
assert_equal(qc.command,
target)
def test_fastqc_notexec():
"""Error thrown if fastqc exe not executable"""
try:
obj = fastqc.FastQC("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_fastqc_exec_notexist():
"""Error thrown if fastqc executable does not exist"""
try:
obj = fastqc.FastQC(os.path.join(".", "fastqc"))
except NotExecutableError:
return True
else:
return False
os.path.join(args.indirname, fname)
for fname in os.listdir(args.indirname)
if fname.startswith(args.prefix)
])
logger.info("Input files: %s" % infilenames)
for fname in infilenames:
if ' ' in os.path.relpath(fname):
logger.error("Relative path to file or directory " +
"'%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)
def test_fastqc():
"""fastqc instantiates with cmd-line if fastqc is in $PATH"""
fastqc.FastQC("fastqc")