Mercurial > repos > jjohnson > cummerbund
diff cuffdata.py @ 1:6a9bc26ab8d9
Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 08 Oct 2012 15:26:47 -0500 |
| parents | |
| children | 9d25b0fd882b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffdata.py Mon Oct 08 15:26:47 2012 -0500 @@ -0,0 +1,73 @@ +""" +CuffData +""" +import logging +import os,os.path,re +import galaxy.datatypes.data +from galaxy.datatypes.images import Html +from galaxy import util +from galaxy.datatypes.metadata import MetadataElement + +log = logging.getLogger(__name__) + +class CuffDiffData( Html ): + """ + CuffDiff output files: + run.info + read_groups.info + cds.count_tracking + cds.diff + cds.fpkm_tracking + cds.read_group_tracking + cds_exp.diff + gene_exp.diff + genes.count_tracking + genes.fpkm_tracking + genes.read_group_tracking + isoform_exp.diff + isoforms.count_tracking + isoforms.fpkm_tracking + isoforms.read_group_tracking + promoters.diff + splicing.diff + tss_group_exp.diff + tss_groups.count_tracking + tss_groups.fpkm_tracking + tss_groups.read_group_tracking + """ + file_ext = 'cuffdata' + 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 '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' + + def regenerate_primary_file(self,dataset): + """ + cannot do this until we are setting metadata + """ + flist = os.listdir(dataset.extra_files_path) + rval = ['<html><head><title>CuffDiff Output</title></head>'] + rval.append('<body>') + rval.append('<p/>CuffDiff Outputs:<p/><ul>') + for i,fname in enumerate(flist): + sfname = os.path.split(fname)[-1] + rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) ) + rval.append( '</ul></body></html>' ) + f = file(dataset.file_name,'w') + f.write("\n".join( rval )) + f.write('\n') + f.close() + + def set_meta( self, dataset, **kwd ): + Html.set_meta( self, dataset, **kwd ) + self.regenerate_primary_file(dataset) + + def sniff( self, filename ): + return False +