Merge pull request #27 from Kalan-Lab/updated-db-downloading

Updated annotation db downloading script

scripts/setup_annotation_dbs.py

@@ -75,23 +75,27 @@ def setup_annot_dbs():
             os.system('rm -rf %s %s' % (download_path + 'profiles/', download_path + 'profiles.tar.gz'))
 
         pgap_info_file = download_path + 'hmm_PGAP.tsv'
-        pgap_hmm_file = download_path + 'PGAP.hmm'
+        pgap_phmm_file = download_path + 'PGAP.hmm'
 
         if not os.path.isfile(pgap_info_file) or not os.path.isfile(pgap_hmm_file):
             # Download PGAP HMMs (Includes TIGR)
             print('Setting up PGAP database!')
             os.system('wget https://ftp.ncbi.nlm.nih.gov/hmm/current/hmm_PGAP.HMM.tgz')
             os.system('wget https://ftp.ncbi.nlm.nih.gov/hmm/current/hmm_PGAP.tsv')
-            os.system('tar -zxvf hmm_PGAP.HMM.tgz')
 
-            assert(os.path.isfile(pgap_info_file))
-            assert(os.path.isdir(download_path + 'hmm_PGAP.HMM/'))
-
-            for f in os.listdir(download_path + 'hmm_PGAP.HMM/'):
-                os.system('cat %s >> %s' % (download_path + 'hmm_PGAP.HMM/' + f, pgap_hmm_file))
-            assert(os.path.isfile(pgap_hmm_file))
+            extract_hmm_dir = 'hmm_PGAP.HMM/'
+            os.mkdir(extract_hmm_dir)
+            os.system(' '.join(['tar', '-zxf', 'hmm_PGAP.HMM.tgz', '-C', 'hmm_PGAP.HMM/']))
+            assert (os.path.isfile(pgap_info_file))
+            assert (os.path.isdir(download_path + 'hmm_PGAP.HMM/'))
+            for folder, subs, files in os.walk(extract_hmm_dir):
+                for filename in files:
+                    if filename.endswith('.HMM') or filename.endswith('.hmm'):
+                        hmm_file_path = os.path.abspath(folder + '/' + filename)
+                        os.system(' '.join(['cat', hmm_file_path, '>>', pgap_phmm_file]))
+            assert(os.path.isfile(pgap_phmm_file))
             listing_handle = open(listing_file, 'a+')
-            listing_handle.write('pgap\t' + pgap_info_file + '\t' + pgap_hmm_file + '\n')
+            listing_handle.write('pgap\t' + pgap_info_file + '\t' + pgap_phmm_file + '\n')
             listing_handle.close()
             os.system('rm -rf %s %s' % (download_path + 'hmm_PGAP.HMM/', download_path + 'hmm_PGAP.HMM.tgz'))
 

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 setup(name='lsaBGC',
-      version='1.39',
+      version='1.40',
       description='Suite for comparative genomic, population genetics and evolutionary analysis, as well as metagenomic mining of micro-evolutionary novelty in BGCs all in the context of a single lineage of interest.',
       url='http://github.com/Kalan-Lab/lsaBGC/',
       author='Rauf Salamzade',