elif i >= 2:
logger.info("Refind the \"parent\" contig from the previous contig for each contig and check they are different")
# We use Exonerate
start_exo_time = time.time()
ExonerateProcess = Aligner.Exonerate(FileteredTrinityFasta, "%s/Trinity_iter_%d.filtered.fasta" % (TmpDirName,i-1) )
# We want to keep only the best hit for each contigs
Exonerate = "%s/iter_%d_%d.exonerate" % (TmpDirName, i-1, i)
ExonerateProcess.Bestn = 1
ExonerateProcess.Model = "est2genome"
# We customize our output format
ExonerateProcess.Ryo = "%ti\t%qi\t%ql\t%qal\t%tal\t%tl\t%pi\n"
ExonerateResult = ExonerateProcess.get_output()
ExonerateFile = open(Exonerate,"w")
ExonerateFile.write(ExonerateResult)
ExonerateFile.close()
AlmostIdenticalResults = ApytramNeeds.check_almost_identical_exonerate_results(ExonerateResult)
if AlmostIdenticalResults and not FinishAllIter:
logger.info("Contigs are almost identical than the previous iteration (Same size (~98%), > 99% identity)")
Stop =True
StatsDict[i]["Exonerate2Time"] = time.time() - start_exo_time
logger.debug("exonerate on previous iter --- %s seconds ---" % (StatsDict[(i)]["Exonerate2Time"]))
# Check that the coverage has inscreased compared to the previous iteration
logger.info("Check that the coverage has inscreased compared to the previous iteration")
# We use Mafft
start_mafft_time = time.time()
MafftProcess = Aligner.Mafft(QueryFile)
MafftProcess.QuietOption = True
MafftProcess.AdjustdirectionOption = True
MafftProcess.AddOption = FileteredTrinityFasta
