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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
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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 def __init__( self, **kwd ):
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44 Html.__init__( self, **kwd )
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45 self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
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46 self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
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47 self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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48 self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
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49 self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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50 self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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51 self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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52 self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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53 self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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54 self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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55 self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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56 self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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57 self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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58 self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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59 self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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60 self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
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61 self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
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62 self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
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63 self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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64 self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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65 self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
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66
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67 def generate_primary_file( self, dataset = None ):
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68 """
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69 This is called only at upload to write the html file
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70 cannot rename the datasets here - they come with the default unfortunately
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71 """
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72 rval = ['<html><head><title>CuffDiff Output</title></head>']
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73 rval.append('<body>')
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74 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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75 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
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76 fn = composite_name
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77 log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
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78 opt_text = ''
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79 if composite_file.optional:
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80 opt_text = ' (optional)'
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81 if composite_file.get('description'):
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82 rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
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83 else:
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84 rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
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85 rval.append( '</ul></body></html>' )
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86 return "\n".join( rval )
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87
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88 def regenerate_primary_file(self,dataset):
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89 """
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90 cannot do this until we are setting metadata
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91 """
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92 flist = os.listdir(dataset.extra_files_path)
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93 rval = ['<html><head><title>CuffDiff Output</title></head>']
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94 rval.append('<body>')
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95 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
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96 for i,fname in enumerate(flist):
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97 sfname = os.path.split(fname)[-1]
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98 rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
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99 rval.append( '</ul></body></html>' )
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100 f = file(dataset.file_name,'w')
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101 f.write("\n".join( rval ))
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102 f.write('\n')
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103 f.close()
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104
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105 def set_meta( self, dataset, **kwd ):
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106 Html.set_meta( self, dataset, **kwd )
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107 self.regenerate_primary_file(dataset)
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108
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109 def sniff( self, filename ):
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110 return False
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111
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112 class CuffDataDB( Binary ):
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113 file_ext = 'cuffdata'
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114 is_binary = True
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115 allow_datatype_change = False
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