Imported stockholm from @bgruening

lib/galaxy/datatypes/msa.py

@@ -1,11 +1,33 @@
 from galaxy.datatypes.data import Text
 from galaxy.datatypes.data import get_file_peek
 from galaxy.datatypes.data import nice_size
+from galaxy.datatypes.metadata import MetadataElement
+import subprocess
+import os
+
 
 import logging
 log = logging.getLogger(__name__)
 
 
+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.
+    """
+    try:
+        cmd = ["grep", "-c"]
+        if invert:
+            cmd.append('-v')
+        cmd.extend([word, filename])
+        out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
+        return int(out.communicate()[0].split()[0])
+    except:
+        pass
+    return 0
+
+
 class Hmmer3( Text ):
     file_ext = "hmm"
 
@@ -29,3 +51,86 @@ def display_peek(self, dataset):
             return dataset.peek
         except:
             return "HMMER3 database (%s)" % ( nice_size( dataset.get_size() ) )
+
+
+class Stockholm_1_0( 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 = 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)