view cuffquant.py @ 0:f7801f8191e0 draft

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"""
Cuffquant format class
"""
import logging
import re
import binascii

from galaxy.ddatatypes.sniff import *
from galaxy.datatypes import data
from galaxy.datatypes.data import Text
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.interval import Gff

log = logging.getLogger(__name__)

class Cuffquant( Binary ):
  """Class describing a CuffQuant output file"""
  file_ext = "cxb"
  def sniff(self,filename):
	# cuffquant cxb file is not documented. the file seems to start with 'serialization::'
	try:
	  header = open(filename).read(23)
	  if header == 'serialization::':
		return True
          return False
        except:
	  return False
  
  def set_peek( self, dataset, is_multi_byte=False):
	if not dataset.dataset.purged:
	  dataset.peek = 'Cuffquant cxb file'
  	  dataset.blurb = data.nice_size( dataset.get_size())
  	else:
	  dataset.peek = 'file does not exist'
	  dataset.blurb = 'file purged from disk'
  def display_peek (self,dataset):
	try:
	  return dataset.peek
	except:
	  return "Cuffquant output file (%s)" % ( data.nice_size( dataset.get_size() ) )  

if hasattr(Binary, 'register_sniffable_binary_format'):
    Binary.register_sniffable_binary_format('cxb', 'cxb', Cuffquant)