/lib/galaxy/datatypes/ngsindex.py
Python | 77 lines | 46 code | 11 blank | 20 comment | 4 complexity | b92b0ae2dcfed0c281de9a731443bb68 MD5 | raw file
1""" 2NGS indexes 3""" 4import os 5import logging 6 7from metadata import MetadataElement 8from images import Html 9 10log = logging.getLogger(__name__) 11 12class BowtieIndex( Html ): 13 """ 14 base class for BowtieIndex 15 is subclassed by BowtieColorIndex and BowtieBaseIndex 16 """ 17 MetadataElement( name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True ) 18 MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True ) 19 20 file_ext = 'bowtie_index' 21 is_binary = True 22 composite_type = 'auto_primary_file' 23 allow_datatype_change = False 24 25 def generate_primary_file( self, dataset = None ): 26 """ 27 This is called only at upload to write the html file 28 cannot rename the datasets here - they come with the default unfortunately 29 """ 30 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' 31 32 def regenerate_primary_file(self,dataset): 33 """ 34 cannot do this until we are setting metadata 35 """ 36 bn = dataset.metadata.base_name 37 flist = os.listdir(dataset.extra_files_path) 38 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)] 39 for i,fname in enumerate(flist): 40 sfname = os.path.split(fname)[-1] 41 rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) ) 42 rval.append( '</ul></html>' ) 43 f = file(dataset.file_name,'w') 44 f.write("\n".join( rval )) 45 f.write('\n') 46 f.close() 47 48 def set_peek( self, dataset, is_multi_byte=False ): 49 if not dataset.dataset.purged: 50 dataset.peek = "Bowtie index file (%s)" % ( dataset.metadata.sequence_space ) 51 dataset.blurb = "%s space" % ( dataset.metadata.sequence_space ) 52 else: 53 dataset.peek = 'file does not exist' 54 dataset.blurb = 'file purged from disk' 55 def display_peek( self, dataset ): 56 try: 57 return dataset.peek 58 except: 59 return "Bowtie index file" 60 def sniff( self, filename ): 61 return False 62 63class BowtieColorIndex( BowtieIndex ): 64 """ 65 Bowtie color space index 66 """ 67 MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True ) 68 69 file_ext = 'bowtie_color_index' 70 71class BowtieBaseIndex( BowtieIndex ): 72 """ 73 Bowtie base space index 74 """ 75 MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True ) 76 77 file_ext = 'bowtie_base_index'