Mercurial > repos > artbio > rsem

annotate rsem.py @ 7:20e2c68f776a draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
author artbio
date Sun, 01 Apr 2018 17:53:57 -0400
parents 39b8e13b1fc9
children ad708409d25e
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1 """
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2 RSEM datatypes
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3 """
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4 import logging
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5 import os
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6 import os.path
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7
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8 from galaxy.datatypes.images import Html
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9 from galaxy.datatypes.metadata import MetadataElement
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10 from galaxy.datatypes.sniff import get_headers
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11 from galaxy.datatypes.tabular import Tabular
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14 log = logging.getLogger(__name__)
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17 class RsemIsoformsResults(Tabular):
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18 file_ext = "rsem.isoforms.results"
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19 """
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20 required columns:
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21 transcript_id gene_id length effective_length expected_count TPM
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22 FPKM IsoPct
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23 optional columns:
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24 pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound
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25 TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound
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26 """
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28 def __init__(self, **kwd):
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29 Tabular.__init__(self, **kwd)
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30 """Initialize RsemResults datatype"""
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31 self.comment_lines = 1
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32
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33 def sniff(self, filename):
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34 headers = get_headers(filename, '\n', count=1)
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35 return (len(headers) > 0 and len(headers[0]) >= 8 and
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36 headers[0][0] == "transcript_id" and
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37 headers[0][1] == "gene_id" and headers[0][6] == "FPKM")
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38
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39 def set_meta(self, dataset, **kwd):
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40 Tabular.set_meta(self, dataset, skip=None, **kwd)
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41
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42
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43 class RsemGenesResults(Tabular):
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44 file_ext = "rsem.genes.results"
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45 """
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46 required columns:
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47 gene_id transcript_id(s) length effective_length expected_count TPM FPKM
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48 optional columns:
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49 pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound
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50 FPKM_ci_lower_bound FPKM_ci_upper_bound
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51 """
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52
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53 def __init__(self, **kwd):
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54 Tabular.__init__(self, **kwd)
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55 """Initialize RsemResults datatype"""
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56 self.comment_lines = 1
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57
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58 def sniff(self, filename):
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59 headers = get_headers(filename, '\n', count=1)
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60 return (len(headers) > 0 and len(headers[0]) >= 7 and
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61 headers[0][0] == "gene_id" and
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62 headers[0][1].startswith("transcript_id") and
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63 headers[0][6] == "FPKM")
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64
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65 def set_meta(self, dataset, **kwd):
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66 Tabular.set_meta(self, dataset, skip=None, **kwd)
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67
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68
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69 class RsemReference(Html):
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70 """Class describing an RSEM reference"""
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71 MetadataElement(name='reference_name', default='rsem_ref',
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72 desc='RSEM Reference Name', readonly=True, visible=True,
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73 set_in_upload=True, no_value='rsem_ref')
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74 file_ext = 'rsem_ref'
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75 allow_datatype_change = False
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76 composite_type = 'auto_primary_file'
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77
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78 def __init__(self, **kwd):
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79 Html.__init__(self, **kwd)
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80 """
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81 Expecting files:
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82 extra_files_path/<reference_name>.grp
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83 extra_files_path/<reference_name>.ti
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84 extra_files_path/<reference_name>.seq
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85 extra_files_path/<reference_name>.transcripts.fa
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86 Optionally includes files:
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87 extra_files_path/<reference_name>.chrlist
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88 extra_files_path/<reference_name>.idx.fa
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89 extra_files_path/<reference_name>.1.ebwt
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90 extra_files_path/<reference_name>.2.ebwt
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91 extra_files_path/<reference_name>.3.ebwt
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92 extra_files_path/<reference_name>.4.ebwt
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93 extra_files_path/<reference_name>.rev.1.ebwt
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94 extra_files_path/<reference_name>.rev.2.ebwt
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95 """
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96 self.add_composite_file('%s.grp', description='Group File',
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97 substitute_name_with_metadata='reference_name',
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98 is_binary=False)
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99 self.add_composite_file('%s.ti', description='',
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100 substitute_name_with_metadata='reference_name',
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101 is_binary=False)
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102 self.add_composite_file('%s.seq', description='',
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103 substitute_name_with_metadata='reference_name',
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104 is_binary=False)
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105 self.add_composite_file('%s.transcripts.fa', description='',
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106 substitute_name_with_metadata='reference_name',
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107 is_binary=False)
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108 self.add_composite_file('%s.chrlist', description='',
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109 substitute_name_with_metadata='reference_name',
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110 is_binary=False, optional=True)
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111 self.add_composite_file('%s.idx.fa', description='',
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112 substitute_name_with_metadata='reference_name',
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113 is_binary=False, optional=True)
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114 self.add_composite_file('%s.1.ebwt', description='',
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115 substitute_name_with_metadata='reference_name',
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116 is_binary=True, optional=True)
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117 self.add_composite_file('%s.2.ebwt', description='',
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118 substitute_name_with_metadata='reference_name',
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119 is_binary=True, optional=True)
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120 self.add_composite_file('%s.3.ebwt', description='',
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121 substitute_name_with_metadata='reference_name',
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122 is_binary=True, optional=True)
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123 self.add_composite_file('%s.4.ebwt', description='',
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124 substitute_name_with_metadata='reference_name',
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125 is_binary=True, optional=True)
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126 self.add_composite_file('%s.rev.1.ebwt', description='',
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127 substitute_name_with_metadata='reference_name',
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128 is_binary=True, optional=True)
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129 self.add_composite_file('%s.rev.2.ebwt', description='',
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130 substitute_name_with_metadata='reference_name',
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131 is_binary=True, optional=True)
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132
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133 def generate_primary_file(self, dataset=None):
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134 """
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135 This is called only at upload to write the file
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136 cannot rename the datasets here - they come with
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137 the default unfortunately
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138 """
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139
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140 def regenerate_primary_file(self, dataset):
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141 """
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142 cannot do this until we are setting metadata
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143 """
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144 link_to_exts = ['.grp', '.ti', '.seq', '.fa', '.chrlist', '.log']
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145 ref_name = dataset.metadata.reference_name
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146 efp = dataset.extra_files_path
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147 flist = os.listdir(efp)
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148 rval = ['<html><head><title>%s</title></head><body><p/>RSEM \
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149 Reference %s files:<p/><ul>' % (dataset.name, ref_name)]
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150 rvalb = []
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151 for i, fname in enumerate(flist):
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152 sfname = os.path.split(fname)[-1]
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153 f, e = os.path.splitext(fname)
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154 if e in link_to_exts:
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155 rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname))
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156 else:
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157 rvalb.append('<li>%s</li>' % (sfname))
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158 if len(rvalb) > 0:
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159 rval += rvalb
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160 rval.append('</ul></body></html>')
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161 fh = file(dataset.file_name, 'w')
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162 fh.write("\n".join(rval))
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163 fh.write('\n')
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164 fh.close()
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165
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166 def set_meta(self, dataset, **kwd):
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167 Html.set_meta(self, dataset, **kwd)
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168 efp = dataset.extra_files_path
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169 flist = os.listdir(efp)
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170 for i, fname in enumerate(flist):
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171 if fname.endswith('.grp'):
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172 dataset.metadata.reference_name = fname[:-4]
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173 break
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174 self.regenerate_primary_file(dataset)
7
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175
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176
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177 class RsemBt2Reference(Html):
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178 """Class describing an RSEM reference"""
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179 MetadataElement(name='reference_name', default='rsem_bt2_ref',
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180 desc='RSEM Bowtie2 Reference Name', readonly=True,
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181 visible=True, set_in_upload=True, no_value='rsem_bt2_ref')
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182 file_ext = 'rsem_bt2_ref'
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183 allow_datatype_change = False
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184 composite_type = 'auto_primary_file'
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185
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186 def __init__(self, **kwd):
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187 Html.__init__(self, **kwd)
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188 """
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189 Expecting files:
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190 extra_files_path/<reference_name>.grp
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191 extra_files_path/<reference_name>.ti
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192 extra_files_path/<reference_name>.seq
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193 extra_files_path/<reference_name>.transcripts.fa
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194 Optionally includes files:
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195 extra_files_path/<reference_name>.chrlist
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196 extra_files_path/<reference_name>.idx.fa
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197 extra_files_path/<reference_name>.n2g.idx.fa
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198 extra_files_path/<reference_name>.1.bt2
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199 extra_files_path/<reference_name>.2.bt2
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200 extra_files_path/<reference_name>.3.bt2
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201 extra_files_path/<reference_name>.4.bt2
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202 extra_files_path/<reference_name>.rev.1.bt2
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203 extra_files_path/<reference_name>.rev.2.bt2
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204 """
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205 self.add_composite_file('%s.grp', description='Group File',
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206 substitute_name_with_metadata='reference_name',
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207 is_binary=False)
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208 self.add_composite_file('%s.ti', description='',
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209 substitute_name_with_metadata='reference_name',
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210 is_binary=False)
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211 self.add_composite_file('%s.seq', description='',
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212 substitute_name_with_metadata='reference_name',
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213 is_binary=False)
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214 self.add_composite_file('%s.transcripts.fa', description='',
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215 substitute_name_with_metadata='reference_name',
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216 is_binary=False)
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217 self.add_composite_file('%s.chrlist', description='',
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218 substitute_name_with_metadata='reference_name',
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219 is_binary=False, optional=True)
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220 self.add_composite_file('%s.idx.fa', description='',
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221 substitute_name_with_metadata='reference_name',
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222 is_binary=False, optional=True)
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223 self.add_composite_file('%s.n2g.idx.fa', description='',
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224 substitute_name_with_metadata='reference_name',
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225 is_binary=False, optional=True)
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226 self.add_composite_file('%s.1.bt2', description='',
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227 substitute_name_with_metadata='reference_name',
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228 is_binary=True, optional=True)
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229 self.add_composite_file('%s.2.bt2', description='',
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230 substitute_name_with_metadata='reference_name',
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231 is_binary=True, optional=True)
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232 self.add_composite_file('%s.3.bt2', description='',
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233 substitute_name_with_metadata='reference_name',
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234 is_binary=True, optional=True)
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235 self.add_composite_file('%s.4.bt2', description='',
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236 substitute_name_with_metadata='reference_name',
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237 is_binary=True, optional=True)
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238 self.add_composite_file('%s.rev.1.bt2', description='',
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239 substitute_name_with_metadata='reference_name',
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240 is_binary=True, optional=True)
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241 self.add_composite_file('%s.rev.2.bt2', description='',
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242 substitute_name_with_metadata='reference_name',
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243 is_binary=True, optional=True)
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244
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245 def generate_primary_file(self, dataset=None):
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246 """
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247 This is called only at upload to write the file
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248 cannot rename the datasets here - they come with
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249 the default unfortunately
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250 """
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251
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252 def regenerate_primary_file(self, dataset):
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253 """
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254 cannot do this until we are setting metadata
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255 """
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256 link_to_exts = ['.grp', '.ti', '.seq', '.fa', '.chrlist', '.log']
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257 ref_name = dataset.metadata.reference_name
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258 efp = dataset.extra_files_path
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259 flist = os.listdir(efp)
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260 rval = ['<html><head><title>%s</title></head><body><p/>RSEM \
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261 Reference %s files:<p/><ul>' % (dataset.name, ref_name)]
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262 rvalb = []
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263 for i, fname in enumerate(flist):
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264 sfname = os.path.split(fname)[-1]
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265 f, e = os.path.splitext(fname)
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266 if e in link_to_exts:
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267 rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname))
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268 else:
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269 rvalb.append('<li>%s</li>' % (sfname))
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270 if len(rvalb) > 0:
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271 rval += rvalb
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272 rval.append('</ul></body></html>')
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273 fh = file(dataset.file_name, 'w')
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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274 fh.write("\n".join(rval))
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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275 fh.write('\n')
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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276 fh.close()
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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277
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278 def set_meta(self, dataset, **kwd):
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279 Html.set_meta(self, dataset, **kwd)
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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280 efp = dataset.extra_files_path
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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281 flist = os.listdir(efp)
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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282 for i, fname in enumerate(flist):
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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283 if fname.endswith('.grp'):
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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284 dataset.metadata.reference_name = fname[:-4]
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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285 break
20e2c68f776a planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 755333360ac6714c4db1eefeffe0bf0a730a94c7
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286 self.regenerate_primary_file(dataset)