BlastnProcess = BlastPlus.Blast("blastn", DatabaseName, BaitSequences)
BlastnProcess.Evalue = Evalue
BlastnProcess.Task = "blastn"
BlastnProcess.Threads = Threads
BlastnProcess.OutFormat = "6 sacc"
# Write read names in ReadNamesFile
ExitCode = BlastnProcess.launch(ReadNamesFile)
StatsDict[(i)]["BlastTime"] = time.time() - start_blast_time
logger.debug("blast --- %s seconds ---" % (StatsDict[(i)]["BlastTime"]))
if PairedData:
# Get paired reads names and remove duplicated names
ExitCode = ApytramNeeds.add_paired_read_names(ReadNamesFile)
else:
# Remove duplicated names
ExitCode = ApytramNeeds.remove_duplicated_read_names(ReadNamesFile)
# Compare the read list names with the list of the previous iteration:
Identical = ApytramNeeds.are_identical(ReadNamesFile,"%s/ReadNames.%d.txt" % (TmpDirName,i-1))
if Identical and not FinishAllIter:
logger.info("Reads from the current iteration are identical than the previous")
Stop = True
IterationNotFinished = True
i -= 1
else:
### Retrieve sequences
logger.info("Retrieve sequences")
ReadFasta = TmpDirName + "/Reads.%d.fasta" % (i)
BlastdbcmdProcess = BlastPlus.Blastdbcmd(DatabaseName, ReadNamesFile, ReadFasta)
# Write read names in ReadNamesFile if the file does not exist
if not os.path.isfile(ReadNamesFile):
(out,err) = BlastnProcess.launch(ReadNamesFile)
else:
logger.warn("%s has already been created, it will be used" %ReadNamesFile )
StatsDict[i]["BlastTime"] = time.time() - start_blast_time
logger.debug("blast --- %s seconds ---" % (StatsDict[i]["BlastTime"]))
if PairedData:
# Get paired reads names and remove duplicated names
logger.info("Get paired reads names and remove duplicated names")
ExitCode = ApytramNeeds.add_paired_read_names(ReadNamesFile)
else:
# Remove duplicated names
logger.info("Remove duplicated names")
out, err = ApytramNeeds.remove_duplicated_read_names(ReadNamesFile)
if err != "\n":
logger.error(err)
# Count the number of reads which will be used in the Trinity assembly
logger.info("Count the number of reads")
StatsDict[i]["ReadsNumber"] = ApytramNeeds.count_lines(ReadNamesFile)
if not StatsDict[i]["ReadsNumber"]:
logger.warning("No read recruted by Blast at the iteration %s" %i)
Stop = True
IterationNotFinished = True
i -= 1
else:
# Compare the read list names with the list of the previous iteration:
Identical = ApytramNeeds.are_identical(ReadNamesFile,"%s/ReadNames.%d.txt" % (TmpDirName,i-1))
