"""
NGS indexes
"""
import logging
from metadata import MetadataElement
from images import Html
log = logging.getLogger(__name__)
class BowtieIndex( Html ):
"""
base class for BowtieIndex
is subclassed by BowtieColorIndex and BowtieBaseIndex
"""
MetadataElement( name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True )
MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True )
file_ext = 'bowtie_index'
is_binary = True
composite_type = 'auto_primary_file'
allow_datatype_change = False
def generate_primary_file( self, dataset = None ):
"""
This is called only at upload to write the html file
cannot rename the datasets here - they come with the default unfortunately
"""
return 'AutoGenerated Primary File for Composite Dataset'
def regenerate_primary_file(self,dataset):
"""
cannot do this until we are setting metadata
"""
bn = dataset.metadata.base_name
flist = os.listdir(dataset.extra_files_path)
rval = ['Files for Composite Dataset %sComprises the following files:' % (bn)]
for i,fname in enumerate(flist):
sfname = os.path.split(fname)[-1]
rval.append( '- %s' % ( sfname, sfname ) )
rval.append( '
' )
f = file(dataset.file_name,'w')
f.write("\n".join( rval ))
f.write('\n')
f.close()
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
dataset.peek = "Bowtie index file (%s)" % ( dataset.metadata.sequence_space )
dataset.blurb = "%s space" % ( dataset.metadata.sequence_space )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def display_peek( self, dataset ):
try:
return dataset.peek
except:
return "Bowtie index file"
def sniff( self, filename ):
return False
class BowtieColorIndex( BowtieIndex ):
"""
Bowtie color space index
"""
MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True )
file_ext = 'bowtie_color_index'
class BowtieBaseIndex( BowtieIndex ):
"""
Bowtie base space index
"""
MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True )
file_ext = 'bowtie_base_index'