diff bim/bim.py @ 0:57bd7c6a72cd draft

planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit 2bf82b5426ec792b408104250a875585cbf7347f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bim/bim.py	Wed Aug 29 08:26:08 2018 -0400
@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+from galaxy import eggs
+
+
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+
+import logging, os, sys, time, sets, tempfile, shutil
+import data
+from galaxy import util
+from galaxy.datatypes.sniff import *
+from cgi import escape
+import urllib
+from bx.intervals.io import *
+from galaxy.datatypes import metadata
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.tabular import Tabular
+
+
+class Bim( Tabular ):
+    """Tab delimited data in bim format"""
+    file_ext = "bim"
+
+    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
+
+
+    def __init__ (self, **kwd):
+        """Initialize bim datatype"""
+        Tabular. __init__ (self, **kwd)
+        self.do_something_else()
+
+
+    def init_meta( self, dataset, copy_from=None ):
+        Tabular.init_meta( self, dataset, copy_from=copy_from )
+        if elems_len == 8:
+            try:
+                map( int, [hdr[6], hdr[7]] )
+                proceed = True
+            except:
+                pass
+
+
+    def sniff( self, filename ):
+        headers = get_headers( filename, '\t' )   
+        try:
+            if len(headers) < 2:
+                return False
+            for hdr in headers:
+                if len( hdr ) > 1 and hdr[0] and not hdr[0].startswith( '#' ):
+                    if len(hdr) != 8:
+                        return False
+                    try:
+                        map( int, [hdr[6], hdr[7]] )
+                    except:
+                        return False
+                # Do other necessary checking here...
+        except:
+            return False
+        # If we haven't yet returned False, then...
+        return True
\ No newline at end of file