def create_database(in_fasta, exe, out_folder):
name = in_fasta.split("/")[-1]
name = re.sub(r'\..*', '',name)
out_name = out_folder + "/" + name
cmd='%s -dbtype nucl -in %s -out %s' %(exe, in_fasta, out_name)
result = getstatusoutput(cmd)
return out_name
def create_database(in_fasta, exe, out_folder):
name = in_fasta.split("/")[-1]
name = re.sub(r'\..*', '', name)
out_name = out_folder + "/" + name
cmd = '%s -dbtype nucl -in %s -out %s' % (exe, in_fasta, out_name)
result = getstatusoutput(cmd)
return out_name
def blast(exe, query, database, percent_id, output_folder):
query_name = re.sub(r'\..*', '',query.split("/")[-1])
db_name = re.sub(r'\..*', '',database.split("/")[-1])
out_name = output_folder + "/" + query_name + "_" + db_name + ".blastout"
cmd = '%s -query %s -db %s -outfmt 6 -perc_identity %s -min_raw_gapped_score %s -out %s' %(exe, query, database, str(percent_id), str(100), out_name)
# print cmd
result= getstatusoutput(cmd)
return out_name
def blast(exe, query, database, percent_id, output_folder):
query_name = re.sub(r'\..*', '', query.split("/")[-1])
db_name = re.sub(r'\..*', '', database.split("/")[-1])
out_name = output_folder + "/" + query_name + "_" + db_name + ".blastout"
cmd = '%s -query %s -db %s -outfmt 6 -perc_identity %s -min_raw_gapped_score %s -out %s' % (
exe, query, database, str(percent_id), str(100), out_name)
# print cmd
result = getstatusoutput(cmd)
return out_name
