Added also version number to mob_hostrange and moved taxa.sqlfile to …

…databases directory as issue #38. Also changed python calls to sys.executable as per issue #39

mob_suite/mob_host_range.py

@@ -7,6 +7,7 @@
 from argparse import ArgumentParser
 from collections import Counter,OrderedDict
 from ete3 import NCBITaxa
+from mob_suite.version import __version__
 
 
 #pandas.options.display.float_format = '{:.1E}'.format #render scientific notation
@@ -301,7 +302,7 @@ def getHostRangeRankCovergence(taxids):
     then traverse the tree and report rank at genus level. Of course this literature based host range prediction might be understatement.
     """
 
-    ncbi = NCBITaxa()
+    ncbi = NCBITaxa(dbfile=os.path.abspath(__file__)+"/databases/taxa.sqlite")
     #taxids=[562,573,1288825,439842]
     tree = ncbi.get_topology(taxids)
     tree.annotate_ncbi_taxa(taxid_attr='name')
@@ -687,7 +688,7 @@ def parse_args():
     parser.add_argument('--outdir', action='store', required=True, help='Output files name prefix')
     parser.add_argument('--inputseq', action='store', required=False, help='Single plasmid sequence in FASTA format (optional)')
     parser.add_argument('--debug', required=False, help='Show debug detailed information (optional)', action='store_true')
-
+    parser.add_argument('-V', '--version', action='version', version="%(prog)s (" + __version__ + ")")
     args = parser.parse_args()
 
 

mob_suite/mob_init.py

@@ -229,7 +229,7 @@ def main():
 
     try:
         logger.info("Init ete3 library ...")
-        os.system('python -c "from ete3 import NCBITaxa; ncbi = NCBITaxa(); ncbi.update_taxonomy_database()"')
+        os.system(sys.executable+' -c "from ete3 import NCBITaxa; ncbi = NCBITaxa(); ncbi.update_taxonomy_database('+database_directory+')"')
     except Exception as e:
         logger.error("Init of ete3 library failed with error {}. Removing lock file".format(e))
         os.remove(lockfilepath)

mob_suite/mob_recon.py

@@ -145,7 +145,7 @@ def run_mob_typer(plasmid_file_abs_path, outdir, num_threads=1,database_dir=None
     logger = logging.getLogger(__name__)
     logger.info("Launching mob_typer to type recently reconstructed plasmid {}".format(plasmid_file_abs_path))
     if database_dir is None:
-        p = Popen(['python', mob_typer_path,
+        p = Popen([sys.executable, mob_typer_path,
                    '--infile', plasmid_file_abs_path,
                    '--outdir', outdir,
                    '--keep_tmp',
@@ -155,7 +155,7 @@ def run_mob_typer(plasmid_file_abs_path, outdir, num_threads=1,database_dir=None
                   stderr=PIPE, universal_newlines=True
                   )
     else:
-        p = Popen(['python', mob_typer_path,
+        p = Popen([sys.executable, mob_typer_path,
                    '--infile', plasmid_file_abs_path,
                    '--outdir', outdir,
                    '--keep_tmp',

mob_suite/tests/test_mob_init.py

@@ -34,7 +34,7 @@ def test_concurrent_init():
                                shell=False
                                )
     except:
-        p1 = subprocess.Popen(['python','../mob_init.py', '-v', '-d', TEST_ROOT+'/run_test/databases'],stdout=subprocess.PIPE,stderr=subprocess.PIPE,
+        p1 = subprocess.Popen([sys.executable,'../mob_init.py', '-v', '-d', TEST_ROOT+'/run_test/databases'],stdout=subprocess.PIPE,stderr=subprocess.PIPE,
                               )
     print("Strated process 1  ...")
     time.sleep(10)
@@ -45,7 +45,7 @@ def test_concurrent_init():
                                stderr=subprocess.PIPE,
                                shell=False)
     except:
-        p2 = subprocess.Popen(['python','../mob_init.py', '-v', '-d', TEST_ROOT+'/run_test/databases'],
+        p2 = subprocess.Popen([sys.executable,'../mob_init.py', '-v', '-d', TEST_ROOT+'/run_test/databases'],
                               stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE,
                               shell=False)

setup.py

@@ -15,6 +15,7 @@
 Programming Language :: Python
 Programming Language :: Python :: 3.5
 Programming Language :: Python :: 3.6
+Programming Language :: Python :: 3.7
 Programming Language :: Python :: Implementation :: CPython
 Operating System :: POSIX :: Linux
 """.strip().split('\n')