try: print "converting,", record = load_genbank(genome_path) except IOError: print "failed to load Genbank file" break else: try: genome_path = dir_in+rec_name+".fas" write_fasta(genome_path, record) except Exception: print "failed to write Fasta file" break try: print "making a DB,", make_blastDB(dbfile_path, genome_path, 'nucl') except IOError: print "failed to make DB" break try: # blastx against each genome DB outfile = blast_out+rec_name+".txt" prefs = {'evalue': 0.001, 'outfmt_pref': 6} print "blasting,", if blast_mode == 'n': local_blastn_2file(infile, dbfile_path, outfile, prefs) elif blast_mode == 'tx': local_tblastx_2file(infile, dbfile_path, outfile, prefs) elif blast_mode == 'tn': local_tblastn_2file(infile, dbfile_path, outfile, prefs) except Exception:
feat_cnt = 0 # cycle through selected features for feat in select: feat_cnt += 1 rec = feat.extract(record) rec.description = genome['name'] + '_' + feat_type + '_' + str( feat_cnt) # initialize or update blast DB if init_DB: ref_records = [value[0] for value in symbolDB.values()] write_fasta(db_file, ref_records) try: make_blastDB(db_path, db_file, 'nucl') except Exception: print "failed to make blast DB" exit() init_DB = False # first go: add all features as new symbols if new_DB: sym_cnt += 1 symbol = 'N' + str(sym_cnt) rec.id = symbol symbolDB[symbol] = [rec] g_vector.append(symbol) else: # tblastn against the reference DB
try: print "converting,", record = load_genbank(genome_path) except IOError: print "failed to load Genbank file" break else: try: genome_path = dir_in + rec_name + ".fas" write_fasta(genome_path, record) except Exception: print "failed to write Fasta file" break try: print "making a DB,", make_blastDB(dbfile_path, genome_path, 'nucl') except IOError: print "failed to make DB" break try: # blastx against each genome DB outfile = blast_out + rec_name + ".txt" prefs = {'evalue': 0.001, 'outfmt_pref': 6} print "blasting,", if blast_mode == 'n': local_blastn_2file(infile, dbfile_path, outfile, prefs) elif blast_mode == 'tx': local_tblastx_2file(infile, dbfile_path, outfile, prefs) elif blast_mode == 'tn': local_tblastn_2file(infile, dbfile_path, outfile, prefs) except Exception:
if feat.type == feat_type] feat_cnt = 0 # cycle through selected features for feat in select: feat_cnt +=1 rec = feat.extract(record) rec.description = genome['name']+'_'+feat_type+'_'+str(feat_cnt) # initialize or update blast DB if init_DB: ref_records = [value[0] for value in symbolDB.values()] write_fasta(db_file, ref_records) try: make_blastDB(db_path, db_file, 'nucl') except Exception: print "failed to make blast DB" exit() init_DB = False # first go: add all features as new symbols if new_DB: sym_cnt +=1 symbol = 'N'+str(sym_cnt) rec.id = symbol symbolDB[symbol] = [rec] g_vector.append(symbol) else: # tblastn against the reference DB