Mercurial > repos > jjohnson > cummerbund
comparison cuffdata.py @ 10:45275147ac1e
Add composite_file defs to datatype
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 17 Oct 2012 12:00:55 -0500 |
| parents | 9d25b0fd882b |
| children | e132e60f95b1 |
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| 9:b6427cdbf6d4 | 10:45275147ac1e |
|---|---|
| 38 """ | 38 """ |
| 39 file_ext = 'cuffdata' | 39 file_ext = 'cuffdata' |
| 40 is_binary = False | 40 is_binary = False |
| 41 composite_type = 'auto_primary_file' | 41 composite_type = 'auto_primary_file' |
| 42 allow_datatype_change = False | 42 allow_datatype_change = False |
| 43 def __init__( self, **kwd ): | |
| 44 Html.__init(self, **kwd ) | |
| 45 self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 46 self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 47 self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 48 self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 49 self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 50 self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 51 self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 52 self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 53 self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 54 self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 55 self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 56 self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 57 self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 58 self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 59 self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 60 self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 61 self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 62 self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 63 self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 64 self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 65 self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False ) | |
| 43 | 66 |
| 44 def generate_primary_file( self, dataset = None ): | 67 def generate_primary_file( self, dataset = None ): |
| 45 """ | 68 """ |
| 46 This is called only at upload to write the html file | 69 This is called only at upload to write the html file |
| 47 cannot rename the datasets here - they come with the default unfortunately | 70 cannot rename the datasets here - they come with the default unfortunately |
| 48 """ | 71 """ |
| 49 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' | 72 rval = ['<html><head><title>CuffDiff Output</title></head>'] |
| 73 rval.append('<body>') | |
| 74 rval.append('<p/>CuffDiff Outputs:<p/><ul>') | |
| 75 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): | |
| 76 fn = composite_name | |
| 77 log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file',fn,composite_file)) | |
| 78 opt_text = '' | |
| 79 if composite_file.optional: | |
| 80 opt_text = ' (optional)' | |
| 81 if composite_file.get('description'): | |
| 82 rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) | |
| 83 else: | |
| 84 rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) ) | |
| 85 rval.append( '</ul></body></html>' ) | |
| 86 return "\n".join( rval ) | |
| 50 | 87 |
| 51 def regenerate_primary_file(self,dataset): | 88 def regenerate_primary_file(self,dataset): |
| 52 """ | 89 """ |
| 53 cannot do this until we are setting metadata | 90 cannot do this until we are setting metadata |
| 54 """ | 91 """ |