view CADDSuite-1.5/galaxyconfigs/molFiles.py @ 7:bfab27640f5e draft

CADDSuite version 1.5

# -*- 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'