changeset 0:b23d89433ee4 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cistrome_phasdb.py	Wed Dec 17 16:07:17 2014 -0500
@@ -0,0 +1,47 @@
+"""
+Cistrome PhasDB datatype
+"""
+import os,os.path,re
+import traceback
+import galaxy.datatypes.data
+from galaxy.datatypes.data import Text
+from galaxy.datatypes.metadata import MetadataElement
+
+class PhasDB( Text ):
+    """Class describing a Cistrome Phascons DB"""
+    """
+    The extrafile path should contain BigWig files with phascons scores for each chromosome "chr" named:  <chr>.bw
+    """
+    file_ext = "cistrome_phasdb"
+    MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=False, visible=True, no_value=None )
+    MetadataElement( name="chromosomes", default=[], desc="Chromosome Names", readonly=True, visible=True, no_value=[], optional=True)
+    composite_type = 'auto_primary_file'
+
+    def __init__( self, **kwd ):
+        Text.__init__( self, **kwd )
+
+    def set_meta( self, dataset, **kwd ):
+        Text.set_meta(self, dataset, **kwd )
+        try:
+            data_dir = dataset.extra_files_path
+            ## search data_dir for bigWig files: ext .bw
+            file_pattern = '(.+).bw'
+            if data_dir and os.path.isdir(data_dir):
+                genome_version = None
+                chromosomes = []
+                for root, dirs, files in os.walk(data_dir):
+                    for fname in files:
+                        m = re.match(file_pattern,fname)
+                        if m:
+                            name = m.groups()[0]
+                            rel_path = root.replace(data_dir,'')
+                            if  rel_path and len(rel_path) > 0:
+                                rel_path = rel_path[1:]
+                                genome_version = rel_path
+                            chromosomes.append(name)
+                            self.add_composite_file( os.path.join(rel_path,fname), description = name, mimetype = 'binary')
+                dataset.metadata.chromosomes = chromosomes
+                if genome_version:
+                    dataset.metadata.genome_version = genome_version
+        except:
+            traceback.print_stack()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Dec 17 16:07:17 2014 -0500
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="cistrome_phasdb.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="cistrome_phasdb" type="galaxy.datatypes.cistrome_phasdb:PhasDB" display_in_upload="True"/>
+    </registration>
+</datatypes>
+