diff infernal.py @ 8:c9e29ac5d099 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"

--- a/infernal.py	Sat Nov 11 16:01:09 2017 -0500
+++ b/infernal.py	Thu Sep 23 19:38:58 2021 +0000
@@ -1,76 +1,88 @@
 # -*- coding: utf-8 -*-
 
-from galaxy.datatypes.data import Text
-from galaxy.datatypes.sniff import get_headers, get_test_fname
-from galaxy.datatypes.data import get_file_peek
+import logging
+import os
 import subprocess
-import os
 
+from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes import metadata
+
 
-def count_special_lines( word, filename, invert = False ):
+def count_special_lines(word, filename, invert=False):
     """
-        searching for special 'words' using the grep tool
-        grep is used to speed up the searching and counting
-        The number of hits is returned.
+    searching for special 'words' using the grep tool
+    grep is used to speed up the searching and counting
+    The number of hits is returned.
     """
     try:
         cmd = ["grep", "-c"]
         if invert:
-            cmd.append('-v')
+            cmd.append("-v")
         cmd.extend([word, filename])
         out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
-def count_lines( filename, non_empty = False):
+
+def count_lines(filename, non_empty=False):
     """
-        counting the number of lines from the 'filename' file
+    counting the number of lines from the 'filename' file
     """
     try:
         if non_empty:
-            out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
+            out = subprocess.Popen(
+                ["grep", "-cve", "^\s*$", filename], stdout=subprocess.PIPE  # noqa W605
+            )
         else:
-            out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
+            out = subprocess.Popen(["wc", "-l", filename], stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
 
-class Infernal_CM_1_1( Text ):
+class Infernal_CM_1_1(Text):
     file_ext = "cm"
 
-    MetadataElement( name="number_of_models", default=0, desc="Number of covariance models", readonly=True, visible=True, optional=True, no_value=0 )
+    MetadataElement(
+        name="number_of_models",
+        default=0,
+        desc="Number of covariance models",
+        readonly=True,
+        visible=True,
+        optional=True,
+        no_value=0,
+    )
 
-    def set_peek( self, dataset, is_multi_byte=False ):
+    def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
-            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            if (dataset.metadata.number_of_models == 1):
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if dataset.metadata.number_of_models == 1:
                 dataset.blurb = "1 model"
             else:
                 dataset.blurb = "%s models" % dataset.metadata.number_of_models
-            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disc'
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"
 
-    def sniff( self, filename ):
+    def sniff(self, filename):
         if count_special_lines("^INFERNAL1/a", filename) > 0:
             return True
         else:
             return False
 
-    def set_meta( self, dataset, **kwd ):
+    def set_meta(self, dataset, **kwd):
         """
         Set the number of models in dataset.
         """
-        dataset.metadata.number_of_models = count_special_lines("^INFERNAL1/a", dataset.file_name)
+        dataset.metadata.number_of_models = count_special_lines(
+            "^INFERNAL1/a", dataset.file_name
+        )
 
-    def split( cls, input_datasets, subdir_generator_function, split_params):
+    def split(cls, input_datasets, subdir_generator_function, split_params):
         """
         Split the input files by model records.
         """
@@ -82,14 +94,17 @@
         input_files = [ds.file_name for ds in input_datasets]
 
         chunk_size = None
-        if split_params['split_mode'] == 'number_of_parts':
-            raise Exception('Split mode "%s" is currently not implemented for CM-files.' % split_params['split_mode'])
-        elif split_params['split_mode'] == 'to_size':
-            chunk_size = int(split_params['split_size'])
+        if split_params["split_mode"] == "number_of_parts":
+            raise Exception(
+                'Split mode "%s" is currently not implemented for CM-files.'
+                % split_params["split_mode"]
+            )
+        elif split_params["split_mode"] == "to_size":
+            chunk_size = int(split_params["split_size"])
         else:
-            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+            raise Exception("Unsupported split mode %s" % split_params["split_mode"])
 
-        def _read_cm_records( filename ):
+        def _read_cm_records(filename):
             lines = []
             with open(filename) as handle:
                 for line in handle:
@@ -97,32 +112,33 @@
                         yield lines
                         lines = [line]
                     else:
-                        lines.append( line )
+                        lines.append(line)
             yield lines
 
-        def _write_part_cm_file( accumulated_lines ):
+        def _write_part_cm_file(accumulated_lines):
             part_dir = subdir_generator_function()
-            part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
-            part_file = open( part_path, 'w' )
-            part_file.writelines( accumulated_lines )
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, "w")
+            part_file.writelines(accumulated_lines)
             part_file.close()
 
         try:
-            cm_records = _read_cm_records( input_files[0] )
+            cm_records = _read_cm_records(input_files[0])
             cm_lines_accumulated = []
-            for counter, cm_record in enumerate( cm_records, start = 1):
-                cm_lines_accumulated.extend( cm_record )
+            for counter, cm_record in enumerate(cm_records, start=1):
+                cm_lines_accumulated.extend(cm_record)
                 if counter % chunk_size == 0:
-                    _write_part_cm_file( cm_lines_accumulated )
+                    _write_part_cm_file(cm_lines_accumulated)
                     cm_lines_accumulated = []
             if cm_lines_accumulated:
-                _write_part_cm_file( cm_lines_accumulated )
-        except Exception,  e:
-            log.error('Unable to split files: %s' % str(e))
+                _write_part_cm_file(cm_lines_accumulated)
+        except Exception as e:
+            logging.error("Unable to split files: %s" % str(e))
             raise
+
     split = classmethod(split)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     Infernal_CM_1_1()
-    Stockholm_1_0()
-
+    # Stockholm_1_0()  # ???