Merge pull request #122 from paulzierep/fix-import

fix bgc_data import issue

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()

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']