def __init__(self, fastq, target_fa):
self.fastq = fastq
self.target_fa = target_fa
self.target_cnt_dic = self.parseTargetList()
self.target_len_dic = self.parseTargetList()
Assm_view = Assm.AssemblyView(path)
Assm_model = Assm.AssemblyModel(fastq, target_fa, Assm_view)
self.Assm_controller = Assm.AssemblyController(Assm_model, Assm_view)
self.pos_str = ''
self.newline_str = '\n'
self.newline_str = '*'
output_path_tmp = os.path.basename(self.fastq).split('.')[0]
self.output_path = '/home/swoo/AWS/output_pyspark_testing/' + output_path_tmp + '_' + str(
os.getpid())
def __init__(self, fastq, target_fa, path_inst):
self.Assm_view = Assm.AssemblyView(path_inst)
self.Assm_model = Assm.AssemblyModel(fastq, target_fa, self.Assm_view)
self.Assm_controller = Assm.AssemblyController(self.Assm_model,
self.Assm_view)
target_fa = 'target_sequences_genomic_dna.fa'
target_fa = 'target_sequences_genomic_dna_XXX.fa'
target_fa = 'target_sequences_barcode_test_short.fa'
target_fa = 'target_sequences_genomic_dna_XXX_sep_wrong.fa'
#target_fa = 'target_sequences_barcode_KRAS_COSM518_diff.fa'
#target_fa = 'target_sequences_barcode_KRAS_COSM522_diff.fa'
#target_fa = 'target_sequences_barcode_KRAS_COSM532_diff.fa'
target_fa = 'target_sequences_genomic_dna_XXX_sep.fa'
target_fa = 'target_sequences_barcode_test.fa'
elif len(sys.argv) < 3:
print('Insufficient arguments')
print('Usage: python XXX.py <FASTQ> <Target_FASTA>')
exit()
elif len(sys.argv) >= 3:
fastq = sys.argv[1]
target_fa = sys.argv[2]
fastq = os.path.join(path.input_dir, fastq)
target_fa = os.path.join(path.input_dir, target_fa)
Assm_view = Assm.AssemblyView(path)
Assm_model = Assm.AssemblyModel(fastq, target_fa, Assm_view)
Assm_controller = Assm.AssemblyController(Assm_model, Assm_view)
start = time.time()
Assm_controller.Process() # Core module
end = time.time()
Assm_view.print_time(start, end)