#Get the available free space of the DB dir
FreeSpaceDBDir = ApytramNeeds.get_free_space(DatabaseDirName)
logger.debug("%s free space in %s" %(FreeSpaceDBDir,DatabaseDirName))
#Concatenate input files
if args.fastq or args.fasta:
if args.fastq:
for fastq in args.fastq:
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):
