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:
logger.error("Paired read names must finished by 1 or 2. %s is uncorrect" %BadReadName)
end(1)
#Build blast formated database from a fasta file
if not os.path.isfile(InputFasta):
logger.error("Error during concatenation or conversion of input files.")
end(1)
# Database building
logger.info(DatabaseName + " database building")
MakeblastdbProcess = BlastPlus.Makeblastdb(InputFasta,DatabaseName)
out,err = MakeblastdbProcess.launch()
CheckDatabase_BlastdbcmdProcess = BlastPlus.Blastdbcmd(DatabaseName, "", "")
if not CheckDatabase_BlastdbcmdProcess.is_database():
