diff lib/galaxy/datatypes/wsf.py @ 0:2c498d40ecde

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/wsf.py	Mon Apr 09 12:03:06 2012 -0400
@@ -0,0 +1,185 @@
+"""
+SnpFile datatype
+"""
+
+import data
+import tempfile
+import os
+import simplejson
+from galaxy import util
+from galaxy.datatypes.sniff import *
+from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.images import Html
+from galaxy.datatypes import metadata
+from galaxy.datatypes.metadata import MetadataElement
+
+class Wped( Html ):
+    allow_datatype_change = False
+    composite_type = 'basic'
+    file_ext = 'wped'
+
+    MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='WpedData', readonly=True, set_in_upload=True )
+
+    def __init__( self, **kwd ):
+        Html.__init__( self, **kwd )
+        self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False )
+        self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )
+
+class Individuals( Tabular ):
+    file_ext = 'ind'
+    def __init__(self, **kwd):
+        Tabular.__init__( self, **kwd )
+        self.column_names = [ 'Column', 'Name', 'Alias' ]
+
+    def display_peek( self, dataset ):
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+
+class DatasetComments( object ):
+    def __init__( self, dataset, comment_string='#' ):
+        self.dataset = dataset
+        self.comment_string = comment_string
+        self.comment_string_len = len(comment_string)
+        self._comments = []
+        self._read_comments()
+
+    def _read_comments( self ):
+        if self.dataset.has_data():
+            try:
+                for line in open(self.dataset.file_name, 'rU'):
+                    if line.startswith(self.comment_string):
+                        comment = line[self.comment_string_len:]
+                        self._comments.append(comment)
+                    else:
+                        break
+            except:
+                pass
+
+    def __str__( self ):
+        return "".join(self._comments)
+
+    @property
+    def comments( self ):
+        return self._comments
+
+class DatasetCommentMetadata( object ):
+    def __init__( self, dataset, comment_string='#' ):
+        self.dataset_comments = DatasetComments( dataset, comment_string )
+        self._comment_metadata = {}
+        self._decode_dataset_comments()
+
+    def _decode_dataset_comments( self ):
+        dataset_comment_string = str( self.dataset_comments )
+        try:
+            self._comment_metadata = simplejson.loads( dataset_comment_string )
+        except simplejson.JSONDecodeError as e:
+            pass
+
+    @property
+    def comment_metadata( self ):
+        return self._comment_metadata
+
+class AnnotatedTabular( Tabular ):
+    """ Tabular file with optional comment block containing JSON to be imported into metadata """
+    MetadataElement( name="comment_metadata", desc="comment metadata", param=metadata.DictParameter, visible=False, readonly=True )
+
+    def set_meta( self, dataset, overwrite = True, **kwd ):
+        Tabular.set_meta( self, dataset, overwrite=overwrite, max_data_lines=None, max_guess_type_data_lines=1000, **kwd )
+        if dataset.metadata.comment_metadata is None:
+            dataset_comment_metadata = DatasetCommentMetadata( dataset )
+            dataset.metadata.comment_metadata = dataset_comment_metadata.comment_metadata.copy()
+            self.set_dataset_metadata_from_comments( dataset )
+
+    def set_dataset_metadata_from_comments( self, dataset ):
+        pass
+
+    def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+        super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte, WIDTH='unlimited', skipchars=['#'] )
+
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, skipchars=['#'] )
+
+class Fake( AnnotatedTabular ):
+    MetadataElement( name="scaffold", desc="scaffold column", param=metadata.ColumnParameter, default=0 )
+    MetadataElement( name="pos", desc="pos column", param=metadata.ColumnParameter, default=0 )
+    MetadataElement( name="ref", desc="ref column", param=metadata.ColumnParameter, default=0 )
+    MetadataElement( name="rPos", desc="rPos column", param=metadata.ColumnParameter, default=0 )
+    MetadataElement( name="species", desc="species", default='', no_value='', visible=False, readonly=True )
+
+    def set_dataset_metadata_from_comments( self, dataset ):
+        self.set_dataset_column_names_metadata( dataset )
+        self.set_dataset_columnParameter_metadata( dataset )
+        self.set_dataset_species_metadata( dataset )
+        self.set_dataset_dbkey_metadata( dataset )
+
+    def set_dataset_column_names_metadata( self, dataset ):
+        value_from_comment_metadata = dataset.metadata.comment_metadata.get( 'column_names', None )
+        if isinstance( value_from_comment_metadata, list ):
+            dataset.metadata.column_names = value_from_comment_metadata[:]
+
+    def set_dataset_columnParameter_metadata( self, dataset ):
+        for name, spec in dataset.metadata.spec.items():
+            if isinstance( spec.param, metadata.ColumnParameter ):
+                value_from_comment_metadata = dataset.metadata.comment_metadata.get( name, None )
+                if value_from_comment_metadata is not None:
+                    try:
+                        i = int( value_from_comment_metadata )
+                    except:
+                        i = 0
+                    if 0 <= i <= dataset.metadata.columns:
+                        setattr( dataset.metadata, name, i )
+
+    def set_dataset_species_metadata( self, dataset ):
+        value_from_comment_metadata = dataset.metadata.comment_metadata.get( 'species', None )
+        if isinstance( value_from_comment_metadata, basestring ):
+            dataset.metadata.species = value_from_comment_metadata
+
+    def set_dataset_dbkey_metadata( self, dataset ):
+        value_from_comment_metadata = dataset.metadata.comment_metadata.get( 'dbkey', '?' )
+        if isinstance( value_from_comment_metadata, basestring ):
+            dataset.metadata.dbkey = value_from_comment_metadata
+
+class SnpFile( Fake ):
+    """ Webb's SNP file format """
+    file_ext = 'wsf'
+
+    MetadataElement( name="individual_names", desc="individual names", visible=False, readonly=True )
+    MetadataElement( name="individual_columns", desc="individual columns", visible=False, readonly=True )
+
+    def set_dataset_metadata_from_comments( self, dataset ):
+        Fake.set_dataset_metadata_from_comments( self, dataset )
+        self.set_dataset_individual_metadata( dataset )
+
+    def set_dataset_individual_metadata( self, dataset ):
+        individual_list = dataset.metadata.comment_metadata.get( 'individuals', None )
+        if not isinstance( individual_list, list ):
+            individual_list = []
+
+        individual_names = []
+        individual_columns = []
+
+        for individual in individual_list:
+            if not isinstance( individual, list ) or len( individual ) != 2:
+                continue
+            name, col = individual
+            if not isinstance( name, basestring ):
+                name = ''
+            try:
+                c = int( col )
+            except:
+                c = 0
+            if 0 < c <= dataset.metadata.columns:
+                individual_names.append( name )
+                individual_columns.append( c )
+
+        if individual_names:
+            dataset.metadata.individual_names = individual_names[:]
+            dataset.metadata.individual_columns = individual_columns[:]
+
+class SapFile( Fake ):
+    """ Webb's SAP file format """
+    file_ext = 'wpf'
+
+    MetadataElement( name="kegg_gene", desc="KEGG gene code column", param=metadata.ColumnParameter, default=0 )
+    MetadataElement( name="kegg_path", desc="KEGG pathway code/name column", param=metadata.ColumnParameter, default=0 )
+