From 174998fc402d19c0a755dec8570157ad5f7b9fe3 Mon Sep 17 00:00:00 2001 From: Kinggerm Date: Wed, 14 Apr 2021 17:52:19 +0800 Subject: [PATCH] v1.7.4 --- GetOrganelleLib/pipe_control_func.py | 20 ++++++++++---------- GetOrganelleLib/versions.py | 4 ++-- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/GetOrganelleLib/pipe_control_func.py b/GetOrganelleLib/pipe_control_func.py index dada842..e335668 100755 --- a/GetOrganelleLib/pipe_control_func.py +++ b/GetOrganelleLib/pipe_control_func.py @@ -316,16 +316,16 @@ def build_bowtie2_db(seed_file, seed_index_base, which_bowtie2, target_echo_name else: sys.stdout.write(this_command + "\n") output, err = building.communicate() - if "unrecognized option" in output.decode("utf8"): - this_command = os.path.join(which_bowtie2, "bowtie2-build") + " --seed " + str(random_seed) + \ - " " + seed_file + " " + seed_index_base - building = subprocess.Popen(this_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) - if not silent and verbose_log: - if log_handler: - log_handler.info(this_command) - else: - sys.stdout.write(this_command + "\n") - output, err = building.communicate() + # if "unrecognized option" in output.decode("utf8"): + # this_command = os.path.join(which_bowtie2, "bowtie2-build") + " --seed " + str(random_seed) + \ + # " " + seed_file + " " + seed_index_base + # building = subprocess.Popen(this_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) + # if not silent and verbose_log: + # if log_handler: + # log_handler.info(this_command) + # else: + # sys.stdout.write(this_command + "\n") + # output, err = building.communicate() if "(ERR)" in output.decode("utf8") or "Error:" in output.decode("utf8"): if log_handler: log_handler.error('\n' + output.decode("utf8")) diff --git a/GetOrganelleLib/versions.py b/GetOrganelleLib/versions.py index e573f03..17189f4 100644 --- a/GetOrganelleLib/versions.py +++ b/GetOrganelleLib/versions.py @@ -16,10 +16,10 @@ def get_versions(): "6. optparse -> argparse (in response to Matthias Bernt@UFZ)", "7. get_organelle_from_assembly.py: fix a bug with the malfunction of --continue when the input is gfa ", "8. get_organelle_from_reads.py/disentangle_organelle_assembly.py: correct typos", - "9. pipe_control_func.py: map_with_bowtie2: warn reads integrity", + "9. pipe_control_func.py: map_with_bowtie2: warn reads integrity; build_bowtie2_db: rm small index", "10. get_organelle_config.py: verbose log for bowtie2 and blast", ], - "time": "2021-04-09 14:00 UTC+8" + "time": "2021-04-14 17:52 UTC+8" }, { "number": "1.7.4-pre2",