Mercurial > repos > jjohnson > cummerbund

annotate cuffdata.py @ 9:b6427cdbf6d4

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Add MAplot and csDendro
author Jim Johnson <jj@umn.edu>
date Fri, 12 Oct 2012 09:56:02 -0500
parents 9d25b0fd882b
children 45275147ac1e
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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.datatypes.binary import Binary
1
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9 from galaxy import util
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10 from galaxy.datatypes.metadata import MetadataElement
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11
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12 log = logging.getLogger(__name__)
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13
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14 class CuffDiffData( Html ):
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15 """
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16 CuffDiff output files:
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17 run.info
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18 read_groups.info
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19 cds.count_tracking
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20 cds.diff
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21 cds.fpkm_tracking
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22 cds.read_group_tracking
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23 cds_exp.diff
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24 gene_exp.diff
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25 genes.count_tracking
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26 genes.fpkm_tracking
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27 genes.read_group_tracking
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28 isoform_exp.diff
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29 isoforms.count_tracking
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30 isoforms.fpkm_tracking
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31 isoforms.read_group_tracking
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32 promoters.diff
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33 splicing.diff
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34 tss_group_exp.diff
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35 tss_groups.count_tracking
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36 tss_groups.fpkm_tracking
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37 tss_groups.read_group_tracking
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38 """
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39 file_ext = 'cuffdata'
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40 is_binary = False
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41 composite_type = 'auto_primary_file'
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42 allow_datatype_change = False
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43
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44 def generate_primary_file( self, dataset = None ):
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45 """
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46 This is called only at upload to write the html file
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47 cannot rename the datasets here - they come with the default unfortunately
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48 """
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49 return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
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50
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51 def regenerate_primary_file(self,dataset):
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52 """
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53 cannot do this until we are setting metadata
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54 """
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55 flist = os.listdir(dataset.extra_files_path)
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56 rval = ['<html><head><title>CuffDiff Output</title></head>']
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57 rval.append('<body>')
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58 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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59 for i,fname in enumerate(flist):
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60 sfname = os.path.split(fname)[-1]
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61 rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
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62 rval.append( '</ul></body></html>' )
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63 f = file(dataset.file_name,'w')
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64 f.write("\n".join( rval ))
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65 f.write('\n')
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66 f.close()
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67
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68 def set_meta( self, dataset, **kwd ):
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69 Html.set_meta( self, dataset, **kwd )
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70 self.regenerate_primary_file(dataset)
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71
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72 def sniff( self, filename ):
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73 return False
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74
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75 class CuffDataDB( Binary ):
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76 file_ext = 'cuffdata'
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77 is_binary = True
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78 allow_datatype_change = False