/lib/galaxy/datatypes/ngsindex.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 77 lines · 46 code · 11 blank · 20 comment · 4 complexity · b92b0ae2dcfed0c281de9a731443bb68 MD5 · raw file 

    

  1. """
    2. 

  2. NGS indexes
    3. 

  3. """
    4. 

  4. import os
    5. 

  5. import logging
    6. 

  6. 

  7. from metadata import MetadataElement
    8. 

  8. from images import Html
    9. 

  9. 

  10. log = logging.getLogger(__name__)
    11. 

  11. 

  12. class BowtieIndex( Html ):
    13. 

  13.     """
    14. 

  14.     base class for BowtieIndex
    15. 

  15.     is subclassed by BowtieColorIndex and BowtieBaseIndex
    16. 

  16.     """
    17. 

  17.     MetadataElement( name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True )
    18. 

  18.     MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True )
    19. 

  19. 

  20.     file_ext = 'bowtie_index'
    21. 

  21.     is_binary = True
    22. 

  22.     composite_type = 'auto_primary_file'
    23. 

  23.     allow_datatype_change = False
    24. 

  24. 

  25.     def generate_primary_file( self, dataset = None ):
    26. 

  26.         """
    27. 

  27.         This is called only at upload to write the html file
    28. 

  28.         cannot rename the datasets here - they come with the default unfortunately
    29. 

  29.         """
    30. 

  30.         return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
    31. 

  31. 

  32.     def regenerate_primary_file(self,dataset):
    33. 

  33.         """
    34. 

  34.         cannot do this until we are setting metadata
    35. 

  35.         """
    36. 

  36.         bn = dataset.metadata.base_name
    37. 

  37.         flist = os.listdir(dataset.extra_files_path)
    38. 

  38.         rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)]
    39. 

  39.         for i,fname in enumerate(flist):
    40. 

  40.             sfname = os.path.split(fname)[-1]
    41. 

  41.             rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) )
    42. 

  42.         rval.append( '</ul></html>' )
    43. 

  43.         f = file(dataset.file_name,'w')
    44. 

  44.         f.write("\n".join( rval ))
    45. 

  45.         f.write('\n')
    46. 

  46.         f.close()
    47. 

  47. 

  48.     def set_peek( self, dataset, is_multi_byte=False ):
    49. 

  49.         if not dataset.dataset.purged:
    50. 

  50.             dataset.peek  = "Bowtie index file (%s)" % ( dataset.metadata.sequence_space )
    51. 

  51.             dataset.blurb = "%s space" % ( dataset.metadata.sequence_space )
    52. 

  52.         else:
    53. 

  53.             dataset.peek = 'file does not exist'
    54. 

  54.             dataset.blurb = 'file purged from disk'
    55. 

  55.     def display_peek( self, dataset ):
    56. 

  56.         try:
    57. 

  57.             return dataset.peek
    58. 

  58.         except:
    59. 

  59.             return "Bowtie index file"
    60. 

  60.     def sniff( self, filename ):
    61. 

  61.         return False
    62. 

  62. 

  63. class BowtieColorIndex( BowtieIndex ):
    64. 

  64.     """
    65. 

  65.     Bowtie color space index
    66. 

  66.     """
    67. 

  67.     MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True )
    68. 

  68. 

  69.     file_ext = 'bowtie_color_index'
    70. 

  70. 

  71. class BowtieBaseIndex( BowtieIndex ):
    72. 

  72.     """
    73. 

  73.     Bowtie base space index
    74. 

  74.     """
    75. 

  75.     MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True )
    76. 

  76. 

  77.     file_ext = 'bowtie_base_index'
    78.