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()