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54
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1 """
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2 HOMER special datatypes
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3 """
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4
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5 from galaxy.datatypes.data import get_file_peek
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6 from galaxy.datatypes.data import Text, Data
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7 from galaxy.datatypes.metadata import MetadataElement
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8 from galaxy.datatypes.images import Html
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9
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10
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11 class TagDirectory(object):
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12 """Base class for HOMER's Tag Directory datatype."""
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13
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14 file_ext = 'homer_tagdir'
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15 composite_type = 'auto_primary_file'
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16 allow_datatype_change = False
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17
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18 def __init__(self, **kwd):
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19 Text.__init__( self, **kwd )
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20 #self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information
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21 self.add_composite_file('tagLengthDistribution.txt', description = 'histogram of read lengths used for alignment', mimetype = 'text/html') # File contains a histogram of read lengths used for alignment.
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22 self.add_composite_file('tagCountDistribution.txt', description = 'histogram of clonal read depth, showing the number of reads per unique position', mimetype = 'text/html') # File contains a histogram of clonal read depth, showing the number of reads per unique position.
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23 self.add_composite_file('tagAutocorrelation.txt', description = 'distribution of distances between adjacent reads in the genome', mimetype = 'text/html') # The autocorrelation routine creates a distribution of distances between adjacent reads in the genome.
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24 self.add_composite_file('tagFreq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads", mimetype = 'text/html', optional=True) # Calculates the nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads.
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25 self.add_composite_file('tagFreqUniq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads (counted only once)", mimetype = 'text/html', optional=True) # Same as tagFreq.txt, however individual genomic positions are only counted once.
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26 self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content.
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27 self.add_composite_file('genomeGCcontent.txt', description = 'Distribution of fragment GC%-content at each location in the genome', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content at each location in the genome.
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28
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29 def generate_primary_file( self, dataset = None ):
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30 rval = ['<html><head><title>HOMER database files</title></head><ul>']
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31 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
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32 opt_text = ''
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33 if composite_file.optional:
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34 opt_text = ' (optional)'
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35 rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) )
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36 rval.append( '</ul></html>' )
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37 return "\n".join( rval )
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38
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39 def display_data(self, trans, data, preview=False, filename=None,
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40 to_ext=None, size=None, offset=None, **kwd):
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41 """Apparently an old display method, but still gets called.
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42
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43 This allows us to format the data shown in the central pane via the "eye" icon.
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44 """
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45 return "This is a HOMER database."
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46
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47 def set_peek( self, dataset, is_multi_byte=False ):
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48 """Set the peek and blurb text."""
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49 if not dataset.dataset.purged:
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50 dataset.peek = "HOMER database (multiple files)"
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51 dataset.blurb = "HOMER database (multiple files)"
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52 else:
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53 dataset.peek = 'file does not exist'
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54 dataset.blurb = 'file purged from disk'
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55
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56 def display_peek( self, dataset ):
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57 """Create HTML content, used for displaying peek."""
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58 try:
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59 return dataset.peek
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60 except:
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61 return "HOMER database (multiple files)"
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62
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63 def get_mime(self):
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64 """Returns the mime type of the datatype (pretend it is text for peek)"""
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65 return 'text/plain'
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66
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67 def merge(split_files, output_file):
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68 """Merge HOMER databases (not implemented)."""
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69 raise NotImplementedError("Merging HOMER databases is not supported")
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70
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71 def split( cls, input_datasets, subdir_generator_function, split_params):
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72 """Split a HOMER database (not implemented)."""
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73 if split_params is None:
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74 return None
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75 raise NotImplementedError("Can't split HOMER databases")
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76
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