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)
# Concatenate fasta files
if len(args.fasta) > 1:
if input_size > FreeSpaceTmpDir:
logger.error("Not enough available free space in %s to concatenate input files" %TmpDirName)
end(1)
InputFasta = "%s/input_fasta.fasta" %(TmpDirName)
logger.info("Concatenate fasta files")
start_convert = time.time()
out,err = ApytramNeeds.cat_fasta(" ".join(args.fasta),InputFasta)
if err:
logger.error(err)
end(1)
logger.info("Concatenation takes %s seconds" %(time.time() - start_convert))
else:
InputFasta = args.fasta[0]
else :
logger.error("The database could not be formatted because fasta files (-fa) or fastq files (-fq) are required!")
end(1)
#Check if the end of sequence name of paired data are 1 or 2
if PairedData:
BadReadName = ApytramNeeds.check_paired_data(InputFasta)
if BadReadName:
