[2] | 1 | """ |
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| 2 | NGS indexes |
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| 3 | """ |
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| 4 | import logging |
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| 5 | from metadata import MetadataElement |
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| 6 | from images import Html |
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| 7 | |
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| 8 | log = logging.getLogger(__name__) |
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| 9 | |
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| 10 | class BowtieIndex( Html ): |
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| 11 | """ |
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| 12 | base class for BowtieIndex |
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| 13 | is subclassed by BowtieColorIndex and BowtieBaseIndex |
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| 14 | """ |
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| 15 | MetadataElement( name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True ) |
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| 16 | MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True ) |
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| 17 | |
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| 18 | file_ext = 'bowtie_index' |
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| 19 | is_binary = True |
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| 20 | composite_type = 'auto_primary_file' |
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| 21 | allow_datatype_change = False |
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| 22 | |
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| 23 | def generate_primary_file( self, dataset = None ): |
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| 24 | """ |
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| 25 | This is called only at upload to write the html file |
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| 26 | cannot rename the datasets here - they come with the default unfortunately |
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| 27 | """ |
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| 28 | return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' |
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| 29 | |
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| 30 | def regenerate_primary_file(self,dataset): |
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| 31 | """ |
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| 32 | cannot do this until we are setting metadata |
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| 33 | """ |
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| 34 | bn = dataset.metadata.base_name |
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| 35 | flist = os.listdir(dataset.extra_files_path) |
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| 36 | rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)] |
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| 37 | for i,fname in enumerate(flist): |
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| 38 | sfname = os.path.split(fname)[-1] |
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| 39 | rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) ) |
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| 40 | rval.append( '</ul></html>' ) |
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| 41 | f = file(dataset.file_name,'w') |
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| 42 | f.write("\n".join( rval )) |
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| 43 | f.write('\n') |
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| 44 | f.close() |
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| 45 | |
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| 46 | def set_peek( self, dataset, is_multi_byte=False ): |
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| 47 | if not dataset.dataset.purged: |
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| 48 | dataset.peek = "Bowtie index file (%s)" % ( dataset.metadata.sequence_space ) |
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| 49 | dataset.blurb = "%s space" % ( dataset.metadata.sequence_space ) |
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| 50 | else: |
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| 51 | dataset.peek = 'file does not exist' |
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| 52 | dataset.blurb = 'file purged from disk' |
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| 53 | def display_peek( self, dataset ): |
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| 54 | try: |
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| 55 | return dataset.peek |
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| 56 | except: |
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| 57 | return "Bowtie index file" |
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| 58 | def sniff( self, filename ): |
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| 59 | return False |
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| 60 | |
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| 61 | class BowtieColorIndex( BowtieIndex ): |
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| 62 | """ |
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| 63 | Bowtie color space index |
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| 64 | """ |
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| 65 | MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True ) |
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| 66 | |
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| 67 | file_ext = 'bowtie_color_index' |
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| 68 | |
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| 69 | class BowtieBaseIndex( BowtieIndex ): |
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| 70 | """ |
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| 71 | Bowtie base space index |
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| 72 | """ |
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| 73 | MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True ) |
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| 74 | |
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| 75 | file_ext = 'bowtie_base_index' |
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