Commit 171276c4 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
Browse files

Compatible again with Python 2, new --label parameter, removed warning

- Fixed incompatibility of recursive glob in Python 2
- Added parameter --label. Will be used in the network_file folder +
visualization dropdown run names
- Removed annoying warning message from last time we broke backwards
compatibility. You are always advised to re-run everything from scratch
while BiG-SCAPE is in pre-release development! But we'll announce loss
of backward compatibility here
parent a2496179
......@@ -401,7 +401,10 @@ def get_gbk_files(inputpath, outputdir, bgc_fasta_folder, min_bgc_size, exclude_
if os.path.isfile(inputpath):
files = [inputpath]
files = glob(os.path.join(inputpath,"**/*.gbk"), recursive=True)
# Unfortunately, this does not work in Python 2:
#files = glob(os.path.join(inputpath,"**/*.gbk"), recursive=True)
files = [os.path.join(dirpath, f) for dirpath, dirnames, files in os.walk(inputpath)
for f in files if f.endswith(".gbk")]
for filepath in files:
file_folder, fname = os.path.split(filepath)
......@@ -1930,6 +1933,10 @@ class FloatRange(object):
def CMD_parser():
parser = ArgumentParser(prog="BiG-SCAPE")
parser.add_argument("-l", "--label", dest="label", help="An extra label for\
this run (will be used as part of the folder name within\
the network_files results)")
parser.add_argument("-i", "--inputdir", dest="inputdir",
help="Input directory of gbk files, if left empty, all \
......@@ -2057,7 +2064,7 @@ def CMD_parser():
compare with the rest of the set (one-VS-all). The \
query BGC does not have to be within inputdir")
parser.add_argument("--version", action="version", version="%(prog)s 201803")
parser.add_argument("--version", action="version", version="%(prog)s 201804")
return parser.parse_args()
......@@ -2199,6 +2206,8 @@ if __name__=="__main__":
start_time = time.localtime()
run_name = "{}{}".format(time.strftime("%Y-%m-%d_%H-%M-%S", start_time), run_mode_string)
if options.label:
run_name = run_name + "_" + options.label
run_data["start_time"] = time.strftime("%d/%m/%Y %H:%M:%S", start_time)
run_data["parameters"] = " ".join(sys.argv[1:])
run_data["input"] = {}
......@@ -2409,22 +2418,6 @@ if __name__=="__main__":
outputfile = os.path.join(domtable_folder,outputbase + '.domtable')
if os.path.isfile(outputfile) and os.path.getsize(outputfile) > 0:
if len(alreadyDone) > 0 and not os.path.isfile(os.path.join(output_folder,"warning_2017-12-06.txt")):
warning_text = " - IMPORTANT NOTICE - \n\
BiG-SCAPE has detected that you are re-using data from a previous \n\
run. However, some sequence identifiers that are used internally \n\
have change to avoid conflicts when using multi-record files (such\n\
as some entries in MIBiG)\n\
If your results were produced after 2017-12-06, please re-run BiG-SCAPE\n\
as usual. If your results are older than this date, please use the \n\
--force_hmmscan parameter.\n\
We are sorry for the inconvenience.\n\
This warning will only appear once.\n"
with open(os.path.join(output_folder,"warning_2017-12-06.txt"), "w") as warning_file:
task_set = fastaFiles - alreadyDone
if len(task_set) == 0:
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