### Check that there is a database else built it
DatabaseName = args.database
CheckDatabase_BlastdbcmdProcess = BlastPlus.Blastdbcmd(DatabaseName, "", "")
if not CheckDatabase_BlastdbcmdProcess.is_database():
logger.info("Database %s does not exist" % DatabaseName)
#Build blast formated database from a fasta file
if args.fastq or args.fasta:
if args.fastq:
if not os.path.isfile(args.fastq):
logger.error("The fastq file (-fq) does not exist.")
sys.exit(1)
else:
# Format the fastq file in fasta
InputFasta = TmpDirName + "/" + os.path.basename(args.fastq) + ".fasta"
logger.info("Convert the fastq file in fasta format")
ExitCode = ApytramNeeds.fastq2fasta(args.fastq,InputFasta)
elif args.fasta:
InputFasta = args.fasta
if not os.path.isfile(InputFasta):
logger.error("The fasta file (-fa) does not exist.")
sys.exit(1)
if os.path.isdir(os.path.dirname(DatabaseName)):
logger.info("Database directory exists")
else:
logger.info("Database directory does not exist, we create it")
os.makedirs(os.path.dirname(DatabaseName))
# database building
logger.info(DatabaseName + " database building")
MakeblastdbProcess = BlastPlus.Makeblastdb(InputFasta,DatabaseName)
ExitCode = MakeblastdbProcess.launch()
if not os.path.isfile(fastq):
logger.error("The fastq file (%s) does not exist." %fastq)
end(1)
# Format the fastq file in fasta
InputFasta = "%s/input_fastq.fasta" %(TmpDirName)
logger.info("Convert the fastq file in fasta format")
start_convert = time.time()
input_size = ApytramNeeds.get_size(args.fastq)
logger.debug("size of input files: %s " %input_size)
if input_size > FreeSpaceTmpDir:
logger.error("Not enough available free space in %s to convert input files" %TmpDirName)
end(1)
if input_size*2 > FreeSpaceDBDir:
logger.error("Not enough available free space in %s to build the database" %DatabaseDirName)
end(1)
out,err = ApytramNeeds.fastq2fasta(" ".join(args.fastq),InputFasta)
if err:
logger.error(err)
end(1)
logger.info("Convertion takes %s seconds" %(time.time() - start_convert))
elif args.fasta:
for fasta in args.fasta:
if not os.path.isfile(fasta):
logger.error("The fasta file (%s) does not exist." %fasta)
end(1)
# Check enough available free space
input_size = ApytramNeeds.get_size(args.fasta)
logger.debug("size of input files: %s " %input_size)
if input_size*2 > FreeSpaceDBDir:
logger.error("Not enough available free space in %s to build the database" %DatabaseDirName)
end(1)