annotate cuffdata.py @ 0:da7241f92ecf

Uploaded

"""
CuffData 
"""
import logging
import os,os.path,re
import galaxy.datatypes.data
from galaxy.datatypes.images import Html
from galaxy.datatypes.binary import Binary
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement

log = logging.getLogger(__name__)

class CuffDiffData( Html ):
    """
    CuffDiff output files:
    run.info
    read_groups.info
    cds.count_tracking
    cds.diff
    cds.fpkm_tracking
    cds.read_group_tracking
    cds_exp.diff
    gene_exp.diff
    genes.count_tracking
    genes.fpkm_tracking
    genes.read_group_tracking
    isoform_exp.diff
    isoforms.count_tracking
    isoforms.fpkm_tracking
    isoforms.read_group_tracking
    promoters.diff
    splicing.diff
    tss_group_exp.diff
    tss_groups.count_tracking
    tss_groups.fpkm_tracking
    tss_groups.read_group_tracking
    """
    file_ext = 'cuffdata'
    is_binary = False
    composite_type = 'auto_primary_file'
    allow_datatype_change = False
    def __init__( self, **kwd ):
        Html.__init__( self, **kwd )
        self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
        self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )

    def generate_primary_file( self, dataset = None ):
        """ 
        This is called only at upload to write the html file
        cannot rename the datasets here - they come with the default unfortunately
        """
        rval = ['<html><head><title>CuffDiff Output</title></head>']
        rval.append('<body>')
        rval.append('<p/>CuffDiff Outputs:<p/><ul>')
        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
            fn = composite_name
            log.debug( "Velvet log info  %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            if composite_file.get('description'):
                rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
            else:
                rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
        rval.append( '</ul></body></html>' )
        return "\n".join( rval )

    def regenerate_primary_file(self,dataset):
        """
        cannot do this until we are setting metadata 
        """
        flist = os.listdir(dataset.extra_files_path)
        rval = ['<html><head><title>CuffDiff Output</title></head>']
        rval.append('<body>')
        rval.append('<p/>CuffDiff Outputs:<p/><ul>')
        for i,fname in enumerate(flist):
            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("\n".join( rval ))
        f.write('\n')
        f.close()

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

    def sniff( self, filename ):
        return False

class CuffDataDB( Binary ):
    file_ext = 'cuffdata'
    is_binary = True
    allow_datatype_change = False