def test_get_file_read_handle(self):
# Read normally
example_fastq = os.path.join(RESOURCE_DIR, EXAMPLE_FASTQ)
f = open(example_fastq, 'r')
d = f.read()
f.close()
# Read original
f = filesys.get_file_read_handle(example_fastq)
d_or = f.read()
f.close()
# Read gz
f = filesys.get_file_read_handle(example_fastq + '.gz')
d_gz = f.read()
f.close()
# Read zip
f = filesys.get_file_read_handle(example_fastq + '.zip')
d_zip = f.read(EXAMPLE_FASTQ)
f.close()
# Test that they are all equal
self.assertTrue(d == d_or and d == d_gz and d == d_zip)
def test_get_file_read_handle(self):
# Read normally
example_fastq = os.path.join(RESOURCE_DIR, EXAMPLE_FASTQ)
f = open(example_fastq,'r')
d = f.read()
f.close()
# Read original
f = filesys.get_file_read_handle(example_fastq)
d_or = f.read()
f.close()
# Read gz
f = filesys.get_file_read_handle(example_fastq + '.gz')
d_gz = f.read()
f.close()
# Read zip
f = filesys.get_file_read_handle(example_fastq + '.zip')
d_zip = f.read(EXAMPLE_FASTQ)
f.close()
# Test that they are all equal
self.assertTrue(d == d_or and d == d_gz and d == d_zip)
def _generate_seqstats(self):
"""
Read in the file and generate stats about the sequences.
"""
fin = filesys.get_file_read_handle(self.fastqfilename)
self.basecount = 0
self.readcount = 0
self.length_hist = {}
for i, line in enumerate(fin):
# If sequence line (line 2 of 4)
if i % 4 == 1:
read_len = len(line.strip())
self.basecount += read_len
self.readcount += 1
# Update histogram
if read_len in self.length_hist:
self.length_hist[read_len] += 1
else:
self.length_hist[read_len] = 1
# Close filehandle
fin.close()
def _generate_seqstats(self):
'''
Read in the file and generate stats about the sequences.
'''
fin = filesys.get_file_read_handle(self.fastqfilename)
self.basecount = 0
self.readcount = 0
self.length_hist = {}
for i, line in enumerate(fin):
# If sequence line (line 2 of 4)
if i % 4 == 1:
read_len = len(line.strip())
self.basecount += read_len
self.readcount += 1
# Update histogram
if read_len in self.length_hist:
self.length_hist[read_len] += 1
else:
self.length_hist[read_len] = 1
# Close filehandle
fin.close()