### 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()
os.makedirs(os.path.dirname(args.output_prefix))
else:
logger.error("The output prefix must be defined")
end(1)
### Check that query files exist
if args.query:
QueryFile = args.query
AliQueryFile = args.query
if not os.path.isfile(QueryFile):
logger.error(QueryFile+" (-q) is not a file.")
end(1)
elif not os.stat(QueryFile).st_size:
logger.error(QueryFile+" (-q) is empty.")
end(1)
elif ApytramNeeds.count_sequences(QueryFile) !=1:
logger.warning("%s (-q) contains more than one query. They are %s sequences." %(QueryFile,ApytramNeeds.count_sequences(QueryFile)))
# If there are multiple probes, align them for the future coverage counter
# Use Mafft
start_mafft_time = time.time()
MafftProcess = Aligner.Mafft(QueryFile)
MafftProcess.QuietOption = True
MafftProcess.AutoOption = True
(MafftResult, err) = MafftProcess.get_output()
AliQueryFile = "%s/References.ali.fasta" %TmpDirName
ApytramNeeds.write_in_file(MafftResult,AliQueryFile)
logger.debug("mafft --- %s seconds ---" % (time.time() - start_mafft_time))
# If the -pep option is used, the -q option must be precised
if args.query_pep:
