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1 """
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2 SnpEff datatypes
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3 """
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4 import os,os.path,re,sys
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5 import galaxy.datatypes.data
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6 from galaxy.datatypes.images import Html
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7 from galaxy.datatypes.metadata import MetadataElement
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8
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9 class RsemReference( Html ):
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10 """Class describing an RSEM reference"""
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11 MetadataElement( name='reference_name', default='galaxy_generated_bowtie_index', desc='RSEM Reference Name', readonly=True, visible=True, no_value=None )
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12
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13 file_ext = 'rsem_ref'
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14 is_binary = True
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15 composite_type = 'auto_primary_file'
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16 allow_datatype_change = False
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17
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18 def generate_primary_file( self, dataset = None ):
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19 """
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20 This is called only at upload to write the html file
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21 cannot rename the datasets here - they come with the default unfortunately
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22 """
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23 return '<html><head></head><body>AutoGenerated Primary File for RSEM Reference Composite Dataset</body></html>'
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24
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25 def regenerate_primary_file(self,dataset):
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26 """
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27 cannot do this until we are setting metadata
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28 """
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29 refname = dataset.metadata.reference_name
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30 flist = os.listdir(dataset.extra_files_path)
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31 rval = ['<html><head><title>RSEM Reference %s</title></head><p/>Comprises the following files:<p/><ul>' % (refname)]
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32 for i,fname in enumerate(flist):
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33 sfname = os.path.split(fname)[-1]
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34 rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) )
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35 rval.append( '</ul></html>' )
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36 f = file(dataset.file_name,'w')
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37 f.write("\n".join( rval ))
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38 f.write('\n')
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39 f.close()
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40
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41 def set_peek( self, dataset, is_multi_byte=False ):
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42 if not dataset.dataset.purged:
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43 dataset.peek = "RSEM Reference (%s)" % ( dataset.metadata.reference_name )
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44 dataset.blurb = "RSEM Reference (%s)" % ( dataset.metadata.reference_name )
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45 else:
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46 dataset.peek = 'RSEM Reference (%s) does not exist' % ( dataset.metadata.reference_name )
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47 dataset.blurb = 'RSEM Reference (%s) purged from disk' % ( dataset.metadata.reference_name )
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48
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49 def display_peek( self, dataset ):
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50 try:
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51 return dataset.peek
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52 except:
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53 return "RSEM Reference"
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54
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55 def set_meta( self, dataset, overwrite = True, **kwd ):
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56 """
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57 Expecting files:
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58 extra_files_path/<reference_name>.grp
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59 extra_files_path/<reference_name>.ti
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60 extra_files_path/<reference_name>.seq
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61 extra_files_path/<reference_name>.transcripts.fa
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62 Optionally includes files:
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63 extra_files_path/<reference_name>.chrlist
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64 extra_files_path/<reference_name>.idx.fa
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65 extra_files_path/<reference_name>.4.ebwt
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66 extra_files_path/<reference_name>.3.ebwt
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67 extra_files_path/<reference_name>.2.ebwt
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68 extra_files_path/<reference_name>.1.ebwt
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69 extra_files_path/<reference_name>.rev.2.ebwt
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70 extra_files_path/<reference_name>.rev.1.ebwt
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71 """
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72 log.info( "RSEM reference set_meta %s %s" % (dataset,dataset.extra_files_path))
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73 pat = '^(.*)\.grp$'
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74 efp = dataset.extra_files_path
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75 flist = os.listdir(efp)
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76 for i,fname in enumerate(flist):
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77 m = re.match(pat,fname)
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78 if m:
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79 dataset.metadata.reference_name = m.groups()[0]
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80 break
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81 self.regenerate_primary_file(dataset)
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82
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83
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