Mercurial > repos > iracooke > proteomics_datatypes
comparison proteomics.py @ 8:6ab4a0bf67df draft
Make splib a composite datatype
| author | iracooke |
|---|---|
| date | Wed, 20 May 2015 00:26:37 -0400 |
| parents | 9cfabf0b942d |
| children | 349af9298ff1 |
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| 7:9cfabf0b942d | 8:6ab4a0bf67df |
|---|---|
| 282 >>> Msp().sniff(fname) | 282 >>> Msp().sniff(fname) |
| 283 False | 283 False |
| 284 """ | 284 """ |
| 285 with open(filename, 'r') as contents: | 285 with open(filename, 'r') as contents: |
| 286 return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:") | 286 return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:") |
| 287 | |
| 288 | |
| 289 class SPLib( Msp ): | |
| 290 """SpectraST Spectral Library. Closely related to msp format""" | |
| 291 file_ext = "splib" | |
| 292 composite_type = 'auto_primary_file' | |
| 293 | |
| 294 def __init__(self, **kwd): | |
| 295 Msp.__init__(self, **kwd) | |
| 296 self.add_composite_file( 'library.splib', | |
| 297 description = 'Spectral Library. Contains actual library spectra', | |
| 298 is_binary = False ) | |
| 299 self.add_composite_file( 'library.spidx', | |
| 300 description = 'Spectrum index', is_binary = False ) | |
| 301 self.add_composite_file( 'library.pepidx', | |
| 302 description = 'Peptide index', is_binary = False) | |
| 303 | |
| 304 | |
| 305 def generate_primary_file( self, dataset = None ): | |
| 306 rval = ['<html><head><title>Spectral Library Composite Dataset </title></head><p/>'] | |
| 307 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') | |
| 308 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): | |
| 309 fn = composite_name | |
| 310 opt_text = '' | |
| 311 if composite_file.optional: | |
| 312 opt_text = ' (optional)' | |
| 313 if composite_file.get('description'): | |
| 314 rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) | |
| 315 else: | |
| 316 rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) ) | |
| 317 rval.append( '</ul></div></html>' ) | |
| 318 return "\n".join( rval ) | |
| 319 | |
| 320 | |
| 321 | |
| 322 def set_peek( self, dataset, is_multi_byte=False ): | |
| 323 """Set the peek and blurb text""" | |
| 324 if not dataset.dataset.purged: | |
| 325 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) | |
| 326 dataset.blurb = 'splib Spectral Library Format' | |
| 327 else: | |
| 328 dataset.peek = 'file does not exist' | |
| 329 dataset.blurb = 'file purged from disk' | |
| 330 | |
| 331 | |
| 332 def sniff(self, filename): | |
| 333 """ Determines whether the file is a SpectraST generated file. | |
| 334 """ | |
| 335 with open(filename, 'r') as contents: | |
| 336 return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "LibID:") | |
| 337 | |
| 287 | 338 |
| 288 class Ms2(Text): | 339 class Ms2(Text): |
| 289 file_ext = "ms2" | 340 file_ext = "ms2" |
| 290 | 341 |
| 291 def sniff(self, filename): | 342 def sniff(self, filename): |