Mercurial > repos > artbio > rsem
comparison rsem.py @ 1:49795544dac7 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 62e8088d5f73cbb9b2f93e23a74636c77a06b492
| author | artbio |
|---|---|
| date | Sun, 01 Apr 2018 18:28:24 -0400 |
| parents | e5e836936d60 |
| children | e00a79cf5f8c |
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| 0:e5e836936d60 | 1:49795544dac7 |
|---|---|
| 170 for i, fname in enumerate(flist): | 170 for i, fname in enumerate(flist): |
| 171 if fname.endswith('.grp'): | 171 if fname.endswith('.grp'): |
| 172 dataset.metadata.reference_name = fname[:-4] | 172 dataset.metadata.reference_name = fname[:-4] |
| 173 break | 173 break |
| 174 self.regenerate_primary_file(dataset) | 174 self.regenerate_primary_file(dataset) |
| 175 | |
| 176 | |
| 177 class RsemBt2Reference(Html): | |
| 178 """Class describing an RSEM reference""" | |
| 179 MetadataElement(name='reference_name', default='rsem_bt2_ref', | |
| 180 desc='RSEM Bowtie2 Reference Name', readonly=True, | |
| 181 visible=True, set_in_upload=True, no_value='rsem_bt2_ref') | |
| 182 file_ext = 'rsem_bt2_ref' | |
| 183 allow_datatype_change = False | |
| 184 composite_type = 'auto_primary_file' | |
| 185 | |
| 186 def __init__(self, **kwd): | |
| 187 Html.__init__(self, **kwd) | |
| 188 """ | |
| 189 Expecting files: | |
| 190 extra_files_path/<reference_name>.grp | |
| 191 extra_files_path/<reference_name>.ti | |
| 192 extra_files_path/<reference_name>.seq | |
| 193 extra_files_path/<reference_name>.transcripts.fa | |
| 194 Optionally includes files: | |
| 195 extra_files_path/<reference_name>.chrlist | |
| 196 extra_files_path/<reference_name>.idx.fa | |
| 197 extra_files_path/<reference_name>.n2g.idx.fa | |
| 198 extra_files_path/<reference_name>.1.bt2 | |
| 199 extra_files_path/<reference_name>.2.bt2 | |
| 200 extra_files_path/<reference_name>.3.bt2 | |
| 201 extra_files_path/<reference_name>.4.bt2 | |
| 202 extra_files_path/<reference_name>.rev.1.bt2 | |
| 203 extra_files_path/<reference_name>.rev.2.bt2 | |
| 204 """ | |
| 205 self.add_composite_file('%s.grp', description='Group File', | |
| 206 substitute_name_with_metadata='reference_name', | |
| 207 is_binary=False) | |
| 208 self.add_composite_file('%s.ti', description='', | |
| 209 substitute_name_with_metadata='reference_name', | |
| 210 is_binary=False) | |
| 211 self.add_composite_file('%s.seq', description='', | |
| 212 substitute_name_with_metadata='reference_name', | |
| 213 is_binary=False) | |
| 214 self.add_composite_file('%s.transcripts.fa', description='', | |
| 215 substitute_name_with_metadata='reference_name', | |
| 216 is_binary=False) | |
| 217 self.add_composite_file('%s.chrlist', description='', | |
| 218 substitute_name_with_metadata='reference_name', | |
| 219 is_binary=False, optional=True) | |
| 220 self.add_composite_file('%s.idx.fa', description='', | |
| 221 substitute_name_with_metadata='reference_name', | |
| 222 is_binary=False, optional=True) | |
| 223 self.add_composite_file('%s.n2g.idx.fa', description='', | |
| 224 substitute_name_with_metadata='reference_name', | |
| 225 is_binary=False, optional=True) | |
| 226 self.add_composite_file('%s.1.bt2', description='', | |
| 227 substitute_name_with_metadata='reference_name', | |
| 228 is_binary=True, optional=True) | |
| 229 self.add_composite_file('%s.2.bt2', description='', | |
| 230 substitute_name_with_metadata='reference_name', | |
| 231 is_binary=True, optional=True) | |
| 232 self.add_composite_file('%s.3.bt2', description='', | |
| 233 substitute_name_with_metadata='reference_name', | |
| 234 is_binary=True, optional=True) | |
| 235 self.add_composite_file('%s.4.bt2', description='', | |
| 236 substitute_name_with_metadata='reference_name', | |
| 237 is_binary=True, optional=True) | |
| 238 self.add_composite_file('%s.rev.1.bt2', description='', | |
| 239 substitute_name_with_metadata='reference_name', | |
| 240 is_binary=True, optional=True) | |
| 241 self.add_composite_file('%s.rev.2.bt2', description='', | |
| 242 substitute_name_with_metadata='reference_name', | |
| 243 is_binary=True, optional=True) | |
| 244 | |
| 245 def generate_primary_file(self, dataset=None): | |
| 246 """ | |
| 247 This is called only at upload to write the file | |
| 248 cannot rename the datasets here - they come with | |
| 249 the default unfortunately | |
| 250 """ | |
| 251 | |
| 252 def regenerate_primary_file(self, dataset): | |
| 253 """ | |
| 254 cannot do this until we are setting metadata | |
| 255 """ | |
| 256 link_to_exts = ['.grp', '.ti', '.seq', '.fa', '.chrlist', '.log'] | |
| 257 ref_name = dataset.metadata.reference_name | |
| 258 efp = dataset.extra_files_path | |
| 259 flist = os.listdir(efp) | |
| 260 rval = ['<html><head><title>%s</title></head><body><p/>RSEM \ | |
| 261 Reference %s files:<p/><ul>' % (dataset.name, ref_name)] | |
| 262 rvalb = [] | |
| 263 for i, fname in enumerate(flist): | |
| 264 sfname = os.path.split(fname)[-1] | |
| 265 f, e = os.path.splitext(fname) | |
| 266 if e in link_to_exts: | |
| 267 rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname)) | |
| 268 else: | |
| 269 rvalb.append('<li>%s</li>' % (sfname)) | |
| 270 if len(rvalb) > 0: | |
| 271 rval += rvalb | |
| 272 rval.append('</ul></body></html>') | |
| 273 fh = file(dataset.file_name, 'w') | |
| 274 fh.write("\n".join(rval)) | |
| 275 fh.write('\n') | |
| 276 fh.close() | |
| 277 | |
| 278 def set_meta(self, dataset, **kwd): | |
| 279 Html.set_meta(self, dataset, **kwd) | |
| 280 efp = dataset.extra_files_path | |
| 281 flist = os.listdir(efp) | |
| 282 for i, fname in enumerate(flist): | |
| 283 if fname.endswith('.grp'): | |
| 284 dataset.metadata.reference_name = fname[:-4] | |
| 285 break | |
| 286 self.regenerate_primary_file(dataset) |