diff --git a/PanACoTA/pangenome_module/mmseqs_functions.py b/PanACoTA/pangenome_module/mmseqs_functions.py index 89d9cd3421cdb33088c451f850d52e4b9ad83b85..6bdfba1fa18af24a35cf6e78718ae45ca52fbb2d 100755 --- a/PanACoTA/pangenome_module/mmseqs_functions.py +++ b/PanACoTA/pangenome_module/mmseqs_functions.py @@ -41,8 +41,9 @@ April 2017 """ import logging import os +import sys import time -import multiprocessing +import threading import progressbar import copy @@ -202,21 +203,27 @@ def do_pangenome(outdir, prt_bank, mmseqdb, min_id, clust_mode, threads, start, "it to a pangenome file.").format(mmseqclust)) else: logger.info("Clustering proteins...") - if not quiet: - widgets = [progressbar.BouncingBar(marker=progressbar.RotatingMarker(markers="◐◓◑◒")), - " - ", progressbar.Timer()] - bar = progressbar.ProgressBar(widgets=widgets, max_value=20, term_width=50) - pool = multiprocessing.Pool(1) - args = [mmseqdb, mmseqclust, tmpdir, logmmseq, min_id, threads, clust_mode] - final = pool.map_async(run_mmseqs_clust, [args], chunksize=1) - pool.close() - if not quiet: - while True: - if final.ready(): - break - bar.update() - bar.finish() - pool.join() + try: + stop_bar = False + if quiet: + widgets = [] + # If not quiet, start a progress bar while clustering proteins. We cannot guess + # how many time it will take, so we start an "infinite" bar, and send it a signal + # when it has to stop. If quiet, we start a thread that will immediatly stop + else: + widgets = [progressbar.BouncingBar(marker=progressbar.RotatingMarker(markers="◐◓◑◒")), + " - ", progressbar.Timer()] + x = threading.Thread(target=utils.thread_progressbar, args=(widgets, lambda : stop_bar,)) + x.start() + args = (mmseqdb, mmseqclust, tmpdir, logmmseq, min_id, threads, clust_mode) + run_mmseqs_clust(args) + except KeyboardInterrupt: # pragma: no cover + stop_bar = True + x.join() + sys.exit(1) + # Clustering done, stop bar and join (if quiet, it was already finished, so we just join it) + stop_bar = True + x.join() # Convert output to tsv file (one line per comparison done) # # Convert output to tsv file (one line per comparison done) # -> returns (families, outfile)