diff --git a/bigscape.py b/bigscape.py index 5bf8f212..296eb19a 100644 --- a/bigscape.py +++ b/bigscape.py @@ -1260,7 +1260,7 @@ def runHmmScan(fastaPath, hmmPath, outputdir, verbose): sys.exit("Error running hmmscan: Fasta file " + fastaPath + " doesn't exist") -def parseHmmScan(hmmscanResults, pfd_folder, pfs_folder, overlapCutoff): +def parseHmmScan(hmmscanResults, pfd_folder, pfs_folder, overlapCutoff, genbankDict): outputbase = ".".join(hmmscanResults.split(os.sep)[-1].split(".")[:-1]) # try to read the domtable file to find out if this gbk has domains. Domains # need to be parsed into fastas anyway. @@ -1960,10 +1960,10 @@ def CMD_parser(): Toggle to activate.") parser.add_argument("-d", "--domain_overlap_cutoff", - dest="domain_overlap_cutoff", default=0.1, help="Specify\ - at which overlap percentage domains are considered to \ - overlap. Domain with the best score is kept \ - (default=0.1).") + dest="domain_overlap_cutoff", default=0.1, + type=float, help="Specify at which overlap percentage \ + domains are considered to overlap. Domain with the best \ + score is kept (default=0.1).") parser.add_argument("-m", "--min_bgc_size", dest="min_bgc_size", default=0, help="Provide the minimum size of a BGC to be included in\ @@ -2519,7 +2519,7 @@ def main(): # Using serialized version for now. Probably doesn't have too bad an impact #pool = Pool(cores,maxtasksperchild=32) for domtableFile in domtableFiles - alreadyDone: - parseHmmScan(domtableFile, pfd_folder, pfs_folder, options.domain_overlap_cutoff) + parseHmmScan(domtableFile, pfd_folder, pfs_folder, options.domain_overlap_cutoff, genbankDict) #pool.apply_async(parseHmmScan, args=(domtableFile,output_folder,options.domain_overlap_cutoff)) #pool.close() #pool.join() diff --git a/setup.py b/setup.py index 57550676..04d85ddc 100644 --- a/setup.py +++ b/setup.py @@ -3,6 +3,7 @@ import os from distutils.core import setup + def generate_package_data(): data_files = [] for directory in ['html_template','Annotated_MIBiG_reference']: @@ -17,10 +18,10 @@ def generate_package_data(): setup( name='bigscape', - version='1.1.5', + version='1.1.8', py_modules=['functions','ArrowerSVG'], - packages=['bigscape'], - package_dir={'bigscape': '.'}, + packages=["bigscape", "bgc_data"], + package_dir={"bigscape": ".", "bgc_data": "."}, package_data=generate_package_data(), entry_points={ 'console_scripts': ['bigscape=bigscape.__main__:main']