diff CADDSuite-1.6/galaxyconfigs/molFiles.py @ 8:dbb480e39d95 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.6/galaxyconfigs/molFiles.py	Sat Dec 15 13:15:46 2012 -0500
@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+class GenericMolFile( data.Text ):
+	file_ext = "mol2/sdf/drf"
+	def check_filetype( self,filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="sdf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="mol2"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="drf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="pdb"
+			return True
+		return False
+
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			if(self.check_filetype(dataset.file_name)) :
+				if (self.no_mols[1] == '1'):
+					dataset.blurb = "1 molecule"
+				else:
+					dataset.blurb = "%s molecules"%self.no_mols[1]
+			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 disk'
+
+	def get_mime(self):
+		return 'text/plain'
+
+
+class GenericMultiMolFile( GenericMolFile ):
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 molecule"
+			else:
+				dataset.blurb = "%s molecules"%self.no_mols[1]
+			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 disk'
+
+class SDF( GenericMultiMolFile ):
+	file_ext = "sdf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class MOL2( GenericMultiMolFile ):
+	file_ext = "mol2"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class DRF( GenericMultiMolFile ):
+	file_ext = "drf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class PDB( GenericMolFile ):
+	file_ext = "pdb"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+	def set_peek( self, dataset, is_multi_byte=False ):
+	#def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
+			dataset.peek = res[1]
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 protein structure"
+			else:
+				dataset.blurb = "%s protein structures"%self.no_mols[1]
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grd ( data.Text ) :
+	file_ext = "grd"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grdtgz ( data.Text ) :
+	file_ext = "grd.tgz"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "compressed score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+