# HG changeset patch # User Jim Johnson # Date 1350493255 18000 # Node ID 45275147ac1e7598835f2e08861cdc5372641774 # Parent b6427cdbf6d4551b654acb1cc3b265ec5cf9555a Add composite_file defs to datatype diff -r b6427cdbf6d4 -r 45275147ac1e cuffdata.py --- a/cuffdata.py Fri Oct 12 09:56:02 2012 -0500 +++ b/cuffdata.py Wed Oct 17 12:00:55 2012 -0500 @@ -40,13 +40,50 @@ is_binary = False composite_type = 'auto_primary_file' allow_datatype_change = False + def __init__( self, **kwd ): + Html.__init(self, **kwd ) + self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) + self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = 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' + rval = ['CuffDiff Output'] + rval.append('') + rval.append('

CuffDiff Outputs:

' ) + return "\n".join( rval ) def regenerate_primary_file(self,dataset): """