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1 """
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2 RSEM datatypes
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3 """
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4 import os,os.path,re,sys
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5 from galaxy.datatypes.data import get_file_peek
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6 from galaxy.datatypes.images import Html
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7 from galaxy.datatypes.tabular import Tabular
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8 from galaxy.datatypes.metadata import MetadataElement
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9 from galaxy.datatypes.sniff import get_headers
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10
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11 import logging
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12
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13 log = logging.getLogger(__name__)
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14
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15 class RsemIsoformsResults( Tabular ):
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16 file_ext = "rsem.isoforms.results"
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17 """
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18 required columns:
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19 transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
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20 optional columns:
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21 pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound
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22 """
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23 def __init__(self, **kwd):
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24 Tabular.__init__( self, **kwd )
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25 """Initialize RsemResults datatype"""
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26 self.comment_lines = 1
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27 def sniff( self, filename ):
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28 headers = get_headers( filename, '\n', count=1 )
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29 return len(headers) > 0 and len(headers[0]) >= 8 and headers[0][0] == "transcript_id" and headers[0][1] == "gene_id" and headers[0][6] == "FPKM"
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30 def set_meta( self, dataset, **kwd ):
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31 Tabular.set_meta( self, dataset, skip=None, **kwd )
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32
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33 class RsemGenesResults( Tabular ):
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34 file_ext = "rsem.genes.results"
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35 """
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36 required columns:
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37 gene_id transcript_id(s) length effective_length expected_count TPM FPKM
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38 optional columns:
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39 pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound
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40 """
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41 def __init__(self, **kwd):
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42 Tabular.__init__( self, **kwd )
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43 """Initialize RsemResults datatype"""
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44 self.comment_lines = 1
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45 def sniff( self, filename ):
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46 headers = get_headers( filename, '\n', count=1 )
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47 return len(headers) > 0 and len(headers[0]) >= 7 and headers[0][0] == "gene_id" and headers[0][1].startswith("transcript_id") and headers[0][6] == "FPKM"
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48 def set_meta( self, dataset, **kwd ):
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49 Tabular.set_meta( self, dataset, skip=None, **kwd )
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50
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51 class RsemReference( Html ):
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52 """Class describing an RSEM reference"""
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53 MetadataElement( name='reference_name', default='rsem_ref' , desc='RSEM Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='rsem_ref' )
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54 file_ext = 'rsem_ref'
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55 allow_datatype_change = False
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56 composite_type = 'auto_primary_file'
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57 def __init__( self, **kwd ):
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58 Html.__init__(self, **kwd)
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59 """
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60 Expecting files:
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61 extra_files_path/<reference_name>.grp
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62 extra_files_path/<reference_name>.ti
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63 extra_files_path/<reference_name>.seq
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64 extra_files_path/<reference_name>.transcripts.fa
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65 Optionally includes files:
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66 extra_files_path/<reference_name>.chrlist
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67 extra_files_path/<reference_name>.idx.fa
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68 extra_files_path/<reference_name>.1.ebwt
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69 extra_files_path/<reference_name>.2.ebwt
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70 extra_files_path/<reference_name>.3.ebwt
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71 extra_files_path/<reference_name>.4.ebwt
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72 extra_files_path/<reference_name>.rev.1.ebwt
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73 extra_files_path/<reference_name>.rev.2.ebwt
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74 """
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75 self.add_composite_file( '%s.grp', description = 'Group File', substitute_name_with_metadata = 'reference_name', is_binary = False )
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76 self.add_composite_file( '%s.ti', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
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77 self.add_composite_file( '%s.seq', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
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78 self.add_composite_file( '%s.transcripts.fa', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
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79 self.add_composite_file( '%s.chrlist', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False, optional=True )
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80 self.add_composite_file( '%s.idx.fa', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False, optional=True )
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81 self.add_composite_file( '%s.1.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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82 self.add_composite_file( '%s.2.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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83 self.add_composite_file( '%s.3.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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84 self.add_composite_file( '%s.4.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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85 self.add_composite_file( '%s.rev.1.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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86 self.add_composite_file( '%s.rev.2.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
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87
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88 def generate_primary_file( self, dataset = None ):
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89 """
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90 This is called only at upload to write the file
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91 cannot rename the datasets here - they come with the default unfortunately
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92 """
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93
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94 def regenerate_primary_file(self,dataset):
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95 """
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96 cannot do this until we are setting metadata
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97 """
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98 link_to_exts = ['.grp','.ti','.seq','.fa','.chrlist','.log']
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99 ref_name = dataset.metadata.reference_name
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100 efp = dataset.extra_files_path
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101 flist = os.listdir(efp)
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102 rval = ['<html><head><title>%s</title></head><body><p/>RSEM Reference %s files:<p/><ul>' % (dataset.name,ref_name)]
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103 rvalb = []
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104 for i,fname in enumerate(flist):
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105 sfname = os.path.split(fname)[-1]
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106 f,e = os.path.splitext(fname)
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107 if e in link_to_exts:
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108 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
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109 else:
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110 rvalb.append( '<li>%s</li>' % (sfname) )
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111 if len(rvalb) > 0:
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112 rval += rvalb
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113 rval.append( '</ul></body></html>' )
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114 fh = file(dataset.file_name,'w')
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115 fh.write("\n".join( rval ))
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116 fh.write('\n')
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117 fh.close()
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118
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119 def set_meta( self, dataset, **kwd ):
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120 Html.set_meta( self, dataset, **kwd )
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121 efp = dataset.extra_files_path
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122 flist = os.listdir(efp)
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123 for i,fname in enumerate(flist):
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124 if fname.endswith('.grp'):
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125 dataset.metadata.reference_name = fname[:-4]
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126 break
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127 self.regenerate_primary_file(dataset)
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128
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