diff --git a/taranis.py b/taranis.py index b30177b..d0cb90a 100755 --- a/taranis.py +++ b/taranis.py @@ -522,7 +522,7 @@ def allele_call_nucleotides ( core_gene_dict_files, reference_query_directory, samples_inferred = [] #allele_list_per_sample = [] for sample_file in sample_dict_files: - print('sample file is: ', sample_file) + #print('sample file is: ', sample_file) #with open (sample_file,'rb') as sample_f : # sample_dict = pickle.load(sample_f) #logger.debug('loaded in memory the sample file %s' , sample_file) @@ -749,10 +749,6 @@ def allele_call_nucleotides ( core_gene_dict_files, reference_query_directory, if not core_name in plot_dict[sample_value] : plot_dict[sample_value][core_name] = [] plot_dict[sample_value][core_name].append([qseqid,sseqid,bitscore,sstart, send, sseq]) - if int(sstart) == length_sseqid or int(send) == length_sseqid: - print( 'PLOT Final') - else: - print ('PLOT inicio') continue else: # print ('There is a deletion of ', gapopen,'gaps', 'or shorter mapping') @@ -815,6 +811,7 @@ def allele_call_nucleotides ( core_gene_dict_files, reference_query_directory, index_delete = deletions_dict[core_name].index(new_sseq) if new_sequence_lenght < query_length : delete_allele = 'ASM_DELETE_' + core_name + '_' + str(index_delete) + print(delete_allele) elif new_sequence_lenght == query_length: delete_allele = 'AEM_DELETE_' + core_name + '_' + str(index_delete) else: