Esempio n. 1
0
### 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()
Esempio n. 2
0
         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)