# 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 to reads from the previous iteration")
Stop = True
IterationNotFinished = True
i -= 1
else:
### Retrieve sequences
if args.database_type in ["RF","FR"]:
logger.info("Split read names depending on 1/ or 2/")
ReadNamesFile_Right = "%s/ReadNames.%d.1.txt" % (TmpDirName,i)
ReadNamesFile_Left = "%s/ReadNames.%d.2.txt" % (TmpDirName,i)
ReadFasta_Right = "%s/Reads.%d.1.fasta" % (TmpDirName,i)
ReadFasta_Left = "%s/Reads.%d.2.fasta" % (TmpDirName,i)
out, err = ApytramNeeds.split_readnames_in_right_left(ReadNamesFile,ReadNamesFile_Right,ReadNamesFile_Left)
if err:
logger.error(err)
StrandList = [".1",".2"]
else:
StrandList = [""]
logger.info("Retrieve reads sequences")
start_blastdbcmd_time = time.time()
for strand in StrandList:
ReadFasta = "%s/Reads.%d%s.fasta" % (TmpDirName,i,strand)
ReadNamesFile = "%s/ReadNames.%d%s.txt" % (TmpDirName,i,strand)
BlastdbcmdProcess = BlastPlus.Blastdbcmd(DatabaseName, ReadNamesFile, ReadFasta)
if not os.path.isfile(ReadFasta):
(out,err) = BlastdbcmdProcess.launch()
else:
