changeset 7:fe8a9ab8daf9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

--- a/data_manager/data_manager_snpsift_dbnsfp.py	Thu Nov 28 15:48:39 2019 -0500
+++ b/data_manager/data_manager_snpsift_dbnsfp.py	Sun Nov 22 12:54:01 2020 +0000
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function
 
 import gzip
 import json
@@ -46,11 +47,6 @@
 dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?'
 
 
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
 def get_nsfp_genome_version(name):
     genome_version = 'hg19'
     dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?'
@@ -66,23 +62,19 @@
 
 def get_annotations(gzip_path):
     annotations = None
-    fh = None
     try:
-        fh = gzip.open(gzip_path, 'r')
-        buf = fh.read(10000)
+        with gzip.open(gzip_path, 'r') as fh:
+            buf = fh.read(10000)
         lines = buf.splitlines()
         headers = lines[0].split('\t')
         annotations = ','.join([x.strip() for x in headers[4:]])
     except Exception as e:
-        stop_err('Error Reading annotations %s : %s' % (gzip_path, e))
-    finally:
-        if fh:
-            fh.close()
+        sys.exit('Error Reading annotations %s : %s' % (gzip_path, e))
     return annotations
 
 
 def tabix_file(input_fname, output_fname):
-    print >> sys.stdout, "tabix_file: %s -> %s" % (input_fname, output_fname)
+    print("tabix_file: %s -> %s" % (input_fname, output_fname))
     ctabix.tabix_compress(input_fname, output_fname, force=True)
     # Column indices are 0-based.
     ctabix.tabix_index(output_fname, seq_col=0, start_col=1, end_col=1)
@@ -119,7 +111,7 @@
                         tfh.close()
                         tempfiles.append(file + "_%d" % len(tempfiles))
                         tfh = open(tempfiles[-1], 'w')
-                        print >> sys.stderr, "%s [%d] pos: %d < %d" % (file, i, pos, lastpos)
+                        print("%s [%d] pos: %d < %d" % (file, i, pos, lastpos), file=sys.stderr)
                     lastpos = pos
                 tfh.write(line)
             tfh.close()
@@ -156,7 +148,8 @@
     (options, args) = parser.parse_args()
 
     filename = args[0]
-    params = json.loads(open(filename).read())
+    with open(filename) as fh:
+        params = json.load(fh)
     target_directory = params['output_data'][0]['extra_files_path']
     if not os.path.exists(target_directory):
         os.mkdir(target_directory)
@@ -182,7 +175,7 @@
         bzip_path = os.path.join(target_directory, bgzip_name)
         db_name = re.sub('(.txt)?.gz$', '', bgzip_name)
     else:
-        stop_err('Either --softgenetics or --dbnsfp_tabular required')
+        sys.exit('Either --softgenetics or --dbnsfp_tabular required')
     if dbnsfp_tsv:
         bgzip_name = '%s.txt.gz' % db_name
         bzip_path = os.path.join(target_directory, bgzip_name)
@@ -195,7 +188,8 @@
     data_manager_dict['data_tables'][data_table].append(data_table_entry)
 
     # save info to json file
-    open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
+    with open(filename, 'w') as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
 
 
 if __name__ == "__main__":

--- a/tool_dependencies.xml	Thu Nov 28 15:48:39 2019 -0500
+++ b/tool_dependencies.xml	Sun Nov 22 12:54:01 2020 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
 <tool_dependency>
     <package name="pysam" version="0.8.3">
-        <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
+        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="08db58be052a"/>
     </package>
 </tool_dependency>
\ No newline at end of file