def test_transcript_with_no_counts(self):
"""If the transcript has no ribocounts, no plot should be produced."""
transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads
output_dir = tempfile.mkdtemp()
parser = riboplot.create_parser()
args = parser.parse_args(['-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir])
self.assertRaises(ribocore.RiboPlotError, riboplot.main, args)
for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
self.assertFalse(os.path.exists(os.path.join(output_dir, fname)))
shutil.rmtree(output_dir)
def test_valid_riboplot_run(self):
"""A good riboplot run"""
output_dir = tempfile.mkdtemp()
print 'Output path is {}'.format(output_dir)
parser = riboplot.create_parser()
args = parser.parse_args(['-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t', CFG.TRANSCRIPT_NAME,
'-o', output_dir])
riboplot.main(args)
for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
self.assertTrue(os.path.exists(os.path.join(output_dir, fname)))
shutil.rmtree(output_dir)
def test_invalid_rna_file(self):
"""If an invalid RNA file is provided, generate an error message"""
# using transcriptome FASTA file as the invalid RNA file for test
parser = riboplot.create_parser()
args = parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-n', CFG.TRANSCRIPTOME_FASTA
])
self.assertRaises(ValueError,
ribocore.check_rna_file,
rna_file=args.rna_file)
def test_transcript_with_no_counts(self):
"""If the transcript has no ribocounts, no plot should be produced."""
transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads
output_dir = tempfile.mkdtemp()
parser = riboplot.create_parser()
args = parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
transcript, '-o', output_dir
])
self.assertRaises(ribocore.RiboPlotError, riboplot.main, args)
for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
self.assertFalse(os.path.exists(os.path.join(output_dir, fname)))
shutil.rmtree(output_dir)
def test_valid_riboplot_run(self):
"""A good riboplot run"""
output_dir = tempfile.mkdtemp()
print 'Output path is {}'.format(output_dir)
parser = riboplot.create_parser()
args = parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-o', output_dir
])
riboplot.main(args)
for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'):
self.assertTrue(os.path.exists(os.path.join(output_dir, fname)))
shutil.rmtree(output_dir)
def test_invalid_rna_file(self):
"""If an invalid RNA file is provided, generate an error message"""
# using transcriptome FASTA file as the invalid RNA file for test
parser = riboplot.create_parser()
args = parser.parse_args(['-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t', CFG.TRANSCRIPT_NAME, '-n', CFG.TRANSCRIPTOME_FASTA])
self.assertRaises(ValueError, ribocore.check_rna_file, rna_file=args.rna_file)
class CheckArgumentsTestCase(unittest.TestCase):
"""Check if all arguments sent on the command line are valid."""
parser = riboplot.create_parser()
def test_bedtools_missing(self):
"""If bedtools is not in PATH, raise an error."""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-n', CFG.RNA_FILE
])
save_path = os.environ['PATH']
os.environ['PATH'] = ''
self.assertRaises(OSError,
ribocore.check_rna_file,
rna_file=args.rna_file)
os.environ['PATH'] = save_path
def test_valid_read_length(self):
"""Read length should be a valid integer."""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '28'
])
ribocore.check_read_lengths(ribo_file=args.ribo_file,
read_lengths=args.read_lengths)
def test_invalid_read_length(self):
"""An error is raised if an invalid read length is used."""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '-1'
]) # invalid read length -1
self.assertRaises(ribocore.ArgumentError,
ribocore.check_read_lengths,
ribo_file=args.ribo_file,
read_lengths=args.read_lengths)
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '100'
]) # invalid read length 100
self.assertRaises(ribocore.RiboPlotError, riboplot.main, args=args)
def test_invalid_read_offset(self):
"""Read offset should be positive."""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-s', '-1'
]) # invalid read offset -1
self.assertRaises(ribocore.ArgumentError,
ribocore.check_read_offsets,
read_offsets=args.read_offsets)
def test_valid_read_lengths_offsets(self):
"""If multiple read lengths, offsets given check if they are valid
i.e., Each read length must have a corresponding offset.
"""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '28,29', '-s', '15,16'
])
ribocore.check_read_lengths_offsets(read_lengths=args.read_lengths,
read_offsets=args.read_offsets)
def test_invalid_read_lengths_offsets(self):
"""If multiple read lengths and offsets are given check if they are valid
i.e., Each read length must have a corresponding offset and vice-versa. If not, raise
an error
"""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '28,29', '-s', '15'
])
self.assertRaises(ribocore.ArgumentError,
ribocore.check_read_lengths_offsets,
read_lengths=args.read_lengths,
read_offsets=args.read_offsets)
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME, '-l', '28', '-s', '15,16'
])
self.assertRaises(ribocore.ArgumentError,
ribocore.check_read_lengths_offsets,
read_lengths=args.read_lengths,
read_offsets=args.read_offsets)
def test_missing_transcript_in_fasta(self):
"""If a transcript is missing in FASTA, an error is raised."""
args = self.parser.parse_args([
'-b', CFG.RIBO_FILE, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME
]) # invalid read offset -1
self.assertRaises(ribocore.ArgumentError,
ribocore.check_required_arguments, args.ribo_file,
args.transcriptome_fasta, 'hello')
def test_missing_transcript_in_bam(self):
"""If a transcript is missing in BAM, an error is raised."""
# testing with an unrelated BAM file
args = self.parser.parse_args([
'-b', CFG.UNRELATED_BAM, '-f', CFG.TRANSCRIPTOME_FASTA, '-t',
CFG.TRANSCRIPT_NAME
])
self.assertRaises(ribocore.ArgumentError,
ribocore.check_required_arguments, args.ribo_file,
args.transcriptome_fasta, args.transcript_name)