Mercurial > repos > bgruening > upload_testing

"""
HOMER special datatypes
"""
import os
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.data import Text, Data
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.images import Html


class TagDirectory( Html ):
    """Base class for HOMER's Tag Directory datatype."""

    file_ext = 'homer_tagdir'
    composite_type = 'auto_primary_file'
    allow_datatype_change = False

    def __init__(self, **kwd):
        Html.__init__( self, **kwd )
        #self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information
        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.
        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.
        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.
        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.
        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.
        self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content.
        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.


    def regenerate_primary_file(self,dataset):
        """
            regenerate the index file after metadata generation
        """
        rval = ['<html><head><title>HOMER database files</title></head>']
        rval.append('<body>')
        rval.append('<p/>CuffDiff Outputs:<p/><ul>')
        for fname in os.listdir(dataset.extra_files_path):
            sfname = os.path.split(fname)[-1]
            rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
        rval.append( '</ul></body></html>' )
        f = file( dataset.file_name, 'w' )
        f.write( '%s\n' % '\n'.join( rval ) )
        f.close()
        if not dataset.info:
            dataset.info = 'HOMER datatype object'
        if not dataset.blurb:
            dataset.blurb = 'Composite file - HOMER'
        return True

    def generate_primary_file( self, dataset = None ):
        rval = ['<html><head><title>HOMER database files</title></head><ul>']
        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) )
        rval.append( '</ul></html>' )
        return "\n".join( rval )

    def set_meta( self, dataset, **kwd ):
        Html.set_meta( self, dataset, **kwd )
        self.regenerate_primary_file(dataset)


    def display_data(self, trans, data, preview=False, filename=None,
                     to_ext=None, size=None, offset=None, **kwd):
        """Apparently an old display method, but still gets called.

        This allows us to format the data shown in the central pane via the "eye" icon.
        """
        return "This is a HOMER database."

    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text."""
        if not dataset.dataset.purged:
            dataset.peek  = "HOMER database (multiple files)"
            dataset.blurb = "HOMER database (multiple files)"
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def display_peek( self, dataset ):
        """Create HTML content, used for displaying peek."""
        try:
            return dataset.peek
        except:
            return "HOMER database (multiple files)"

    def get_mime(self):
        """Returns the mime type of the datatype (pretend it is text for peek)"""
        return 'text/plain'

    def merge(split_files, output_file):
        """Merge HOMER databases (not implemented)."""
        raise NotImplementedError("Merging HOMER databases is not supported")

    def split( cls, input_datasets, subdir_generator_function, split_params):
        """Split a HOMER database (not implemented)."""
        if split_params is None:
            return None
        raise NotImplementedError("Can't split HOMER databases")
author	bgruening
date	Tue, 13 Aug 2013 09:38:07 -0400 (2013-08-13)
parents	07a5042bbe90
children