ApytramNeeds.write_in_file(MafftResult,AliQueryFile)
logger.debug("mafft --- %s seconds ---" % (time.time() - start_mafft_time))
# If the -pep option is used, the -q option must be precised
if args.query_pep:
if not os.path.isfile(args.query_pep):
logger.error(args.query_pep+" (-pep) is not a file.")
end(1)
if not args.query:
logger.error("-pep option must be accompanied of the query in nucleotide format (-q option)")
end(1)
#Get the available free space of the tmp dir
FreeSpaceTmpDir = ApytramNeeds.get_free_space(TmpDirName)
logger.debug("%s free space in %s" %(FreeSpaceTmpDir,TmpDirName))
### Check that there is a database, otherwise build it
DatabaseName = args.database
CheckDatabase_BlastdbcmdProcess = BlastPlus.Blastdbcmd(DatabaseName, "", "")
if not CheckDatabase_BlastdbcmdProcess.is_database():
logger.info("Database %s does not exist" % DatabaseName)
DatabaseDirName = os.path.dirname(DatabaseName)
if os.path.isdir(DatabaseDirName) or not DatabaseDirName :
logger.info("Database directory exists")
else:
logger.info("Database directory does not exist, we create it")
os.makedirs(DatabaseDirName)
