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 parseAndProcessCSVPyspark(self, line):
if line.startswith('Features'):
return '' # if header line, return
molecule_model = Assm.MoleculeModel(self.Assm_controller.Assm_model)
if self.fastq.endswith('.csv'):
self.putIntoMolecule(line, molecule_model)
elif self.fastq.endswith('.tsv'):
self.putIntoMoleculeTSV(line, molecule_model)
else: # Unknown file format
return
if self.Assm_controller.Assm_model.ParseModel.checkInsufficientSixmers(molecule_model):
return ''
origin_gene, MTM_ambig = self.Assm_controller.determineTargetGene(molecule_model)
if MTM_ambig == True:
self.Assm_controller.MTM_removed_cnt += 1
return ''
elif origin_gene.startswith('XXX') and not param.show_XXX_targets():
self.Assm_controller.XXX_removed_cnt += 1
return ''
elif self.Assm_controller.Assm_model.ParseModel.checkInsufficientTargets(self.Assm_controller.Assm_model, molecule_model, origin_gene):
return '' # Check if we have enough candidate targets
molecule_model.initMutationGraph(origin_gene) # Charlie's Mutation-Graph-factory
self.Assm_controller.estimateAllCov(molecule_model, origin_gene)
# self.updateReadCounts(molecule_model, position) ### Update info ###
if param.enable_blind_mu():
self.Assm_controller.FindMutations(molecule_model, origin_gene)
molecule_model.Graph.GraphTrimming(self.Assm_controller.Assm_model.trimming_threshold)
molecule_model.Graph.CallInsertions(self.Assm_controller.Assm_model.trimming_threshold)
if param.fast_path():
molecule_model.Graph.grdQualityPath(0)
else:
molecule_model.Graph.optPath()
### Update info ###
position = ''
self.updateInfo(molecule_model, position)
FASTA_str = self.genFASTAstr(molecule_model.Graph, self.pos_str ,origin_gene)
cov_list = self.genCOVstr(molecule_model.Graph)
# cov_list = self.genCOVlist(molecule_model.Graph)
VCF_list = ''
VCF_list = ['']
del molecule_model ### free molecule_model instance ###
# cov_list = [int(1000*random.random()) for i in xrange(1)]
# VCF_list = [int(1000*random.random()) for i in xrange(5)]
# tmp_list2 = [int(1000*random.random()) for i in xrange(5)]
return FASTA_str, origin_gene, cov_list, VCF_list
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)