Mercurial > repos > bgruening > upload_testing
diff homer.py @ 55:e9cd105a8856
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 12 Aug 2013 09:06:47 -0400 |
| parents | 675d25a0b9d4 |
| children | 07a5042bbe90 |
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--- a/homer.py Mon Aug 12 08:16:21 2013 -0400 +++ b/homer.py Mon Aug 12 09:06:47 2013 -0400 @@ -8,7 +8,7 @@ from galaxy.datatypes.images import Html -class TagDirectory(object): +class TagDirectory( Text ): """Base class for HOMER's Tag Directory datatype.""" file_ext = 'homer_tagdir' @@ -26,6 +26,29 @@ self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content. self.add_composite_file('genomeGCcontent.txt', description = 'Distribution of fragment GC%-content at each location in the genome', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content at each location in the genome. + + 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 ): + Text.set_meta( self, dataset, **kwd ) + self.regenerate_primary_file(dataset) + + def generate_primary_file( self, dataset = None ): rval = ['<html><head><title>HOMER database files</title></head><ul>'] for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():