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
