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)
BlastdbcmdProcess.launch()
### Launch Trinity
