def test_prevalidate_submission_with_invalid_data():
"""prevalidate: prevalidate_submission with invalid data"""
# first a simple sequence of the proper length
vi = prevalidate_submission('MONKEY!')
assert vi is not None
assert not vi.valid
assert vi.problem is not None
assert "doesn't look like" in vi.problem
def test_prevalidate_submission_with_valid_data():
"""prevalidate: prevalidate_submission with valid data"""
# first a simple sequence of the proper length
vi = prevalidate_submission('AGCT'*90)
assert vi is not None
assert vi.valid
assert vi.looks_like is not None
assert "dna" == vi.looks_like
# next some fasta looking thing
vi = prevalidate_submission('>a_sequence\nAGCTTGA')
assert vi is not None
assert vi.valid
assert vi.looks_like is not None
assert "fasta" == vi.looks_like
# next some sites
vi = prevalidate_submission('16223, 16129A 16234+C')
assert vi is not None
assert vi.valid
assert vi.looks_like is not None
assert "sites" == vi.looks_like
def run_command():
"""Perform automated human mtDNA haplotype identification."""
# Set up the options parser
usage = "usage: %prog [options] sequence|filename"
parser = OptionParser(usage=usage)
parser.add_option(
'-f',
'--file',
action='store_true',
default=False,
help='load sequences from FASTA file',
dest='use_file')
parser.add_option(
'-c',
'--csv',
action='store_true',
dest='csv',
default=False,
help='output in comma-separated-value format')
parser.add_option(
'-n',
'--no-csv-header',
action='store_false',
dest='csv_header',
default=True,
help='output a csv header')
parser.add_option(
'-o',
'--out',
dest='outfile',
help='write results to FILE',
default=False,
metavar='FILE')
# Parse the options
(options, args) = parser.parse_args()
# At least one argument is always required.
# It will be either the sequence to be tested, or
# When the -f flag is used, the filename of the fasta file
# to be tested
if len(args) != 1:
if options.use_file:
print 'You must provide a filename!'
print "Type 'mitotype -h' for help."
else:
print 'You must provide a sequence to test'
print "Type 'mitotype -h' for help."
sys.exit(1)
# If we've made it this far we're probably going to have to do some
# actual work; initialize the matcher.
hvrm = HVRMatcher()
# Do the work, either:
# (1) load the fasta file
# (2) use sequence passed on the command line
working_text = ''
if options.use_file:
if os.path.exists(args[0]):
f = open(args[0], 'r')
working_text = f.read()
f.close()
else:
print 'ERROR: Could not find file: %s' % args[0]
sys.exit(1)
else:
working_text = args[0]
vi = prevalidate_submission(working_text)
if not vi.valid:
print 'ERROR: Could not validate input: %s' % vi.problem
results = hvrm.match(working_text, vi)
# If outfile option is used, make stdout point to that file
if options.outfile:
outf = open(options.outfile, 'w')
sys.stdout = outf
# If we're outputing to CSV, spit out a header
if options.csv and options.csv_header:
print 'Query Label,Query Defining Positions,Motif Label,Match Score,Motif Defining Positions,Source'
# Output the results
for r in results:
if options.csv:
for row in r.csv_rows():
print row
else:
print r
sys.stdout.flush()
