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annotate cuffdata.py @ 1:6a9bc26ab8d9

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Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
author Jim Johnson <jj@umn.edu>
date Mon, 08 Oct 2012 15:26:47 -0500
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children 9d25b0fd882b
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6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
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1 """
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2 CuffData
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3 """
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4 import logging
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5 import os,os.path,re
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6 import galaxy.datatypes.data
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7 from galaxy.datatypes.images import Html
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8 from galaxy import util
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9 from galaxy.datatypes.metadata import MetadataElement
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10
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11 log = logging.getLogger(__name__)
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12
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13 class CuffDiffData( Html ):
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14 """
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15 CuffDiff output files:
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16 run.info
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17 read_groups.info
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18 cds.count_tracking
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19 cds.diff
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20 cds.fpkm_tracking
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21 cds.read_group_tracking
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22 cds_exp.diff
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23 gene_exp.diff
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24 genes.count_tracking
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25 genes.fpkm_tracking
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26 genes.read_group_tracking
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27 isoform_exp.diff
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28 isoforms.count_tracking
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29 isoforms.fpkm_tracking
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30 isoforms.read_group_tracking
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31 promoters.diff
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32 splicing.diff
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33 tss_group_exp.diff
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34 tss_groups.count_tracking
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35 tss_groups.fpkm_tracking
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36 tss_groups.read_group_tracking
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37 """
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38 file_ext = 'cuffdata'
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39 is_binary = True
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40 composite_type = 'auto_primary_file'
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41 allow_datatype_change = False
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42
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43 def generate_primary_file( self, dataset = None ):
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44 """
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45 This is called only at upload to write the html file
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46 cannot rename the datasets here - they come with the default unfortunately
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47 """
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48 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
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49
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50 def regenerate_primary_file(self,dataset):
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51 """
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52 cannot do this until we are setting metadata
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53 """
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54 flist = os.listdir(dataset.extra_files_path)
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55 rval = ['<html><head><title>CuffDiff Output</title></head>']
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56 rval.append('<body>')
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57 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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58 for i,fname in enumerate(flist):
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59 sfname = os.path.split(fname)[-1]
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60 rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
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61 rval.append( '</ul></body></html>' )
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62 f = file(dataset.file_name,'w')
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63 f.write("\n".join( rval ))
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64 f.write('\n')
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65 f.close()
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66
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67 def set_meta( self, dataset, **kwd ):
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68 Html.set_meta( self, dataset, **kwd )
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69 self.regenerate_primary_file(dataset)
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70
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71 def sniff( self, filename ):
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72 return False
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73