if not args.no_last_iter_file:
# Last iteration seqeunces
ExitCode = ApytramNeeds.write_apytram_output(FileteredTrinityFasta,
TrinityExonerateResultsDict,
OutPrefixName+".fasta",
Header = TrinityExonerateProcess.Ryo.replace('%',"").replace("\n","").split(),
Names = FilteredSequenceNames)
# Stats files
start_output_stat = time.time()
if args.stats:
logger.info("Write statistics file (OutPrefix.stats.csv)")
ApytramNeeds.write_stats(StatsDict,OutPrefixName)
if args.plot:
logger.info("Create plot from the statistics file (OutPrefix.stats.pdf)")
ApytramNeeds.create_plot(StatsDict, OutPrefixName)
logger.debug("Writing stats file --- %s seconds ---" % (time.time() - start_output_stat))
if args.plot_ali:
start_output_ali = time.time()
logger.info("Create plot from the statistics file (OutPrefix.ali.png)")
ApytramNeeds.create_plot_ali(DicPlotCov, OutPrefixName)
logger.debug("Writing alignment plot --- %s seconds ---" % (time.time() - start_output_ali))
else:
logger.warn("No results")
### Remove tempdir if the option --tmp have not been use
if not args.tmp:
logger.debug("Remove the temporary directory")
#Remove the temporary directory :
if "tmp_apytram" in TmpDirName:
