diff infernal.py @ 10:0bffd4183326 draft

Uploaded

--- a/infernal.py	Sat Sep 07 16:14:02 2013 -0400
+++ b/infernal.py	Sun Sep 08 05:08:20 2013 -0400
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-from galaxy.datatypes import data
+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 subprocess
@@ -41,90 +41,7 @@
     return 0
 
 
-class Stockholm_1_0( data.text ):
-    file_ext = "stockholm"
-
-    MetadataElement( name="number_of_alignments", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0 )
-
-    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.blurb = "1 alignment"
-            else:
-                dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
-            dataset.peek = data.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'
-
-    def sniff( self, filename ):
-        if count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', filename) > 0:
-            return True
-        else:
-            return False
-
-    def set_meta( self, dataset, **kwd ):
-        """
-
-        Set the number of models in dataset.
-        """
-        dataset.metadata.number_of_models = count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
-
-    def split( cls, input_datasets, subdir_generator_function, split_params):
-        """
-
-        Split the input files by model records.
-        """
-        if split_params is None:
-            return None
-
-        if len(input_datasets) > 1:
-            raise Exception("STOCKHOLM-file splitting does not support multiple files")
-        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 STOCKHOLM-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'])
-
-        def _read_stockholm_records( filename ):
-            lines = []
-            with open(filename) as handle:
-                for line in handle:
-                    lines.append( line )
-                    if line.strip() == '//':
-                        yield lines
-                        lines = []
-
-        def _write_part_stockholm_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_file.close()
-
-        try:
-
-            stockholm_records = _read_stockholm_records( input_files[0] )
-            stockholm_lines_accumulated = []
-            for counter, stockholm_record in enumerate( stockholm_records, start = 1):
-                stockholm_lines_accumulated.extend( stockholm_record )
-                if counter % chunk_size == 0:
-                    _write_part_stockholm_file( stockholm_lines_accumulated )
-                    stockholm_lines_accumulated = []
-            if stockholm_lines_accumulated:
-                _write_part_stockholm_file( stockholm_lines_accumulated )
-        except Exception,  e:
-            log.error('Unable to split files: %s' % str(e))
-            raise
-    split = classmethod(split)
-
-
-class Infernal_CM_1_1( data.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 )
@@ -205,3 +122,7 @@
             raise
     split = classmethod(split)
 
+if __name__ == '__main__':
+    Infernal_CM_1_1()
+    Stockholm_1_0()
+