def check_db(which_blast=""):
global options
in_index = options.reference_fa_base + '.index'
if options.reference_fa_base:
time0 = time.time()
ref_fasta = read_fasta(options.reference_fa_base)
if len(ref_fasta[0]) > 1:
options.reference_fa_base += '.1st.fasta'
write_fasta(out_file=options.reference_fa_base,
matrix=[[ref_fasta[0][0]], [ref_fasta[1][0]],
ref_fasta[2]],
overwrite=True)
sys.stdout.write(
'\nWarning: multi-seqs in reference file, only use the 1st sequence.'
)
elif len(ref_fasta[0]) == 0:
sys.stdout.write('\nError: illegal reference file!')
exit()
make_blast_db(input_file=options.reference_fa_base,
output_base=in_index,
which_blast=which_blast)
sys.stdout.write('\nMaking BLAST db cost ' + str(time.time() - time0))
else:
sys.stdout.write('\nError: No reference input!')
exit()
return in_index
def check_db(reference_fa_base, which_blast=""):
in_index = reference_fa_base + '.index'
if min([os.path.exists(in_index+postfix) for postfix in ('.nhr', '.nin', '.nsq')]):
pass
elif reference_fa_base:
print('Making BLAST db ... ')
make_blast_db(input_file=reference_fa_base, output_base=in_index, which_blast=which_blast)
print('Making BLAST db finished.')
else:
print('ERROR: No reference input!')
exit()
return in_index
def initialize_notation_database(which_blast, overwrite=False):
for fasta_f in os.listdir(NOT_DIR):
if fasta_f.endswith(".fasta") and fasta_f[:-6] in ("embplant_pt", "other_pt", "embplant_mt", "embplant_nr",
"animal_mt", "fungus_mt"):
fasta_f = os.path.join(NOT_DIR, fasta_f)
output_base = remove_db_postfix(fasta_f)
sys.stdout.write("makeblastdb " + output_base + " ... ")
sys.stdout.flush()
if overwrite or sum([os.path.exists(output_base + postfix) for postfix in (".nhr", ".nin", ".nsq")]) != 3:
make_blast_db(input_file=fasta_f,
output_base=output_base,
which_blast=which_blast)
sys.stdout.write("finished\n")
else:
sys.stdout.write("skipped\n")
def initialize_notation_database(which_blast, fasta_f, overwrite=False):
# blast index
output_base = remove_db_postfix(fasta_f)
sys.stdout.write("makeblastdb " + os.path.basename(fasta_f) + " ... ")
sys.stdout.flush()
if overwrite or sum([
os.path.exists(output_base + postfix)
for postfix in (".nhr", ".nin", ".nsq")
]) != 3:
make_blast_db(input_file=fasta_f,
output_base=output_base,
which_blast=which_blast)
sys.stdout.write("finished\n")
else:
sys.stdout.write("skipped\n")