root/galaxy-central/lib/galaxy/datatypes/genetics.py @ 2

"""
rgenetics datatypes 
Use at your peril
Ross Lazarus
for the rgenetics and galaxy projects 

genome graphs datatypes derived from Interval datatypes
genome graphs datasets have a header row with appropriate columnames
The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps
subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or 'NA') values
ross lazarus for rgenetics
august 20 2007
"""

import logging, os, sys, time, tempfile, shutil, string, glob
import data
from galaxy import util
from cgi import escape
import urllib, binascii
from galaxy.web import url_for
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.data import Text
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.images import Html
from galaxy.datatypes.interval import Interval
from galaxy.util.hash_util import *

gal_Log = logging.getLogger(__name__)
verbose = False

class GenomeGraphs( Tabular ):
    """
    Tab delimited data containing a marker id and any number of numeric values
    """

    MetadataElement( name="markerCol", default=1, desc="Marker ID column", param=metadata.ColumnParameter )
    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
    MetadataElement( name="column_types", default=[], desc="Column types", readonly=True, visible=False )
    file_ext = 'gg'

    def __init__(self, **kwd):
        """
        Initialize gg datatype, by adding UCSC display apps
        """
        Tabular.__init__(self, **kwd)
        self.add_display_app ( 'ucsc', 'Genome Graph', 'as_ucsc_display_file', 'ucsc_links' )    

    
    def set_meta(self,dataset,**kwd):
        Tabular.set_meta( self, dataset, **kwd)
        dataset.metadata.markerCol = 1
        header = file(dataset.file_name,'r').readlines()[0].strip().split('\t')
        dataset.metadata.columns = len(header)
        t = ['numeric' for x in header]
        t[0] = 'string'
        dataset.metadata.column_types = t
        return True

    def as_ucsc_display_file( self, dataset, **kwd ):
        """
        Returns file
        """
        return file(dataset.file_name,'r')

    def ucsc_links( self, dataset, type, app, base_url ):
        """ 
        from the ever-helpful angie hinrichs angie@soe.ucsc.edu
        a genome graphs call looks like this 
        http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname
        &hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
        &hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=
        &hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index
        &hgGenome_doSubmitUpload=submit
                Galaxy gives this for an interval file
        http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText=
        http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc
        """
        ret_val = []
        ggtail = 'hgGenome_doSubmitUpload=submit'
        if not dataset.dbkey:
              dataset.dbkey = 'hg18' # punt!
        if dataset.has_data():
              for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey):
                    if site_name in app.config.ucsc_display_sites:
                        site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
                        internal_url = "%s" % url_for( controller='dataset',
                                dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
                        display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) 
                        display_url = urllib.quote_plus( display_url )
                        # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
                        #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
                        sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
                        #sl.append("&hgt.customText=%s")
                        sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
                        sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
                        sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
                        sl.append("&hgGenome_doSubmitUpload=submit")
                        sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
                        s = ''.join(sl)
                        s = urllib.quote_plus(s)
                        redirect_url = s
                        log.debug('## rg gg ucsc rdurl=%s; s = %s' % (redirect_url,s))
                        link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
                        ret_val.append( (site_name, link) )
        return ret_val

    def make_html_table( self, dataset, skipchars=[] ):
        """
        Create HTML table, used for displaying peek
        """
        npeek = 5
        out = ['<table cellspacing="0" cellpadding="3">']
        f = open(dataset.file_name,'r')
        d = f.readlines()[:5]
        if len(d) == 0:
            out = "Cannot find anything to parse in %s" % dataset.name
            return out
        hasheader = 0
        try:
            test = ['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics
        except:
            hasheader = 1
        try:
            # Generate column header
            out.append( '<tr>' )
            if hasheader:
               for i, name in enumerate(d[0].split() ):
                  out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
               d.pop(0)
               out.append('</tr>')
            for row in d:
               out.append('<tr>')
               out.append(''.join(['<td>%s</td>' % x for x in row.split()]))
               out.append('</tr>')
            out.append( '</table>' )
            out = "".join( out )
        except Exception, exc:
            out = "Can't create peek %s" % exc
        return out
        
    def validate( self, dataset ):
        """
        Validate a gg file - all numeric after header row
        """
        errors = list()
        infile = open(dataset.file_name, "r")
        header= infile.next() # header
        for i,row in enumerate(infile):
           ll = row.strip().split('\t')[1:] # first is alpha feature identifier
           badvals = []
           for j,x in enumerate(ll):
              try:
                x = float(x)
              except:
                badval.append('col%d:%s' % (j+1,x))
        if len(badvals) > 0:
            errors.append('row %d, %s' % (' '.join(badvals)))
            return errors 
        
    def sniff( self, filename ):
        """
        Determines whether the file is in gg format
        """
        f = open(filename,'r')
        headers = f.readline().split()
        rows = [f.readline().split()[1:] for x in range(3)] # small sample
        #headers = get_headers( filename, '\t' )
        for row in rows:
            try:
                nums = [float(x) for x in row] # first col has been removed
            except:
                return false
        return true

    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'application/vnd.ms-excel'


class rgTabList(Tabular):
    """ 
    for sampleid and for featureid lists of exclusions or inclusions in the clean tool
    featureid subsets on statistical criteria -> specialized display such as gg
    """    
    file_ext = "rgTList"


    def __init__(self, **kwd):
        """
        Initialize featurelistt datatype
        """
        Tabular.__init__( self, **kwd )
        self.column_names = []

    def make_html_table( self, dataset, skipchars=[] ):
        """
        Create HTML table, used for displaying peek
        """
        out = ['<table cellspacing="0" cellpadding="3">']
        comments = []
        try:
            # Generate column header
            out.append( '<tr>' )
            for i, name in enumerate( self.column_names ):
                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
            if dataset.metadata.columns - len( self.column_names ) > 0:
                for i in range( len( self.column_names ), dataset.metadata.columns ):
                    out.append( '<th>%s</th>' % str( i+1 ) )
                out.append( '</tr>' )
            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
            out.append( '</table>' )
            out = "".join( out )
        except Exception, exc:
            out = "Can't create peek %s" % exc
        return out

    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'text/html'


class rgSampleList(rgTabList):
    """ 
    for sampleid exclusions or inclusions in the clean tool
    output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,...
    since they can be uploaded, should be flexible
    but they are persistent at least
    same infrastructure for expression?
    """    
    file_ext = "rgSList"

    def __init__(self, **kwd):
        """
        Initialize samplelist datatype
        """
        rgTabList.__init__( self, **kwd )
        self.column_names[0] = 'FID'
        self.column_names[1] = 'IID'
        # this is what Plink wants as at 2009
   
    def sniff(self,filename):
        infile = open(dataset.file_name, "r")
        header= infile.next() # header
        if header[0] == 'FID' and header[1] == 'IID':
            return True
        else:
            return False
        
class rgFeatureList( rgTabList ):
    """
    for featureid lists of exclusions or inclusions in the clean tool
    output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,...
    featureid subsets on statistical criteria -> specialized display such as gg
    same infrastructure for expression?
    """    
    file_ext = "rgFList"

    def __init__(self, **kwd):
        """Initialize featurelist datatype"""
        rgTabList.__init__( self, **kwd )
        for i,s in enumerate(['#FeatureId', 'Chr', 'Genpos', 'Mappos']):
            self.column_names[i] = s
 

class Rgenetics(Html):      
    """
    base class to use for rgenetics datatypes
    derived from html - composite datatype elements
    stored in extra files path
    """
   
    MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='RgeneticsData',
    readonly=True, set_in_upload=True)
    
    composite_type = 'auto_primary_file'
    allow_datatype_change = False
    file_ext = 'rgenetics'

    def generate_primary_file( self, dataset = None ):
        rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>']
        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
            fn = composite_name
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            if composite_file.get('description'):
                rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
            else:
                rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
        rval.append( '</ul></div></html>' )
        return "\n".join( rval )

    def regenerate_primary_file(self,dataset):
        """
        cannot do this until we are setting metadata 
        """
        bn = dataset.metadata.base_name
        efp = dataset.extra_files_path
        flist = os.listdir(efp)
        rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)]
        for i,fname in enumerate(flist):
            sfname = os.path.split(fname)[-1] 
            f,e = os.path.splitext(fname)
            rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
        rval.append( '</ul></body></html>' )
        f = file(dataset.file_name,'w')
        f.write("\n".join( rval ))
        f.write('\n')
        f.close()

    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'text/html'


    def set_meta( self, dataset, **kwd ):

        """
        for lped/pbed eg

        """
        Html.set_meta( self, dataset, **kwd )
        if kwd.get('overwrite') == False:
            if verbose:
                gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
            return True
        try:
            efp = dataset.extra_files_path
        except: 
            if verbose:                
               gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
            return False
        try:
            flist = os.listdir(efp)
        except:
            if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
            return False
        if len(flist) == 0:
            if verbose:
                gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
            return False
        self.regenerate_primary_file(dataset)
        if not dataset.info:           
                dataset.info = 'Galaxy genotype datatype object'
        if not dataset.blurb:
               dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
        return True



class SNPMatrix(Rgenetics):
    """
    BioC SNPMatrix Rgenetics data collections
    """
    file_ext="snpmatrix"

    def set_peek( self, dataset, **kwd ):
        if not dataset.dataset.purged:
            dataset.peek  = "Binary RGenetics file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
            
    def sniff(self,filename):
        """ need to check the file header hex code
        """
        infile = open(dataset.file_name, "b")
        head = infile.read(16)
        head = [hex(x) for x in head]
        if head <> '':
            return False
        else:
            return True


class Lped(Rgenetics):
    """
    linkage pedigree (ped,map) Rgenetics data collections
    """
    file_ext="lped"
    
    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False )
        self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )


class Pphe(Rgenetics):
    """
    Plink phenotype file - header must have FID\tIID... Rgenetics data collections
    """
    file_ext="pphe"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = False )




class Fphe(Rgenetics):
    """
    fbat pedigree file - mad format with ! as first char on header row
    Rgenetics data collections
    """
    file_ext="fphe"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.fphe', description = 'FBAT Phenotype File', substitute_name_with_metadata = 'base_name' )

class Phe(Rgenetics):
    """
    Phenotype file
    """
    file_ext="phe"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name',
             is_binary = False )



class Fped(Rgenetics):
    """
    FBAT pedigree format - single file, map is header row of rs numbers. Strange.
    Rgenetics data collections
    """
    file_ext="fped"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name',
              is_binary = False )


class Pbed(Rgenetics):
    """
    Plink Binary compressed 2bit/geno Rgenetics data collections
    """
    file_ext="pbed"
    
    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
        self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
        self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )

class ldIndep(Rgenetics):
    """
    LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno
    This is really a plink binary, but some tools work better with less redundancy so are constrained to
    these files
    """
    file_ext="ldreduced"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
        self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
        self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )


class Eigenstratgeno(Rgenetics):
    """
    Eigenstrat format - may be able to get rid of this
    if we move to shellfish
    Rgenetics data collections
    """
    file_ext="eigenstratgeno"
    
    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = False )
        self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = False )
        self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = False )
        


class Eigenstratpca(Rgenetics):
    """
    Eigenstrat PCA file for case control adjustment
    Rgenetics data collections
    """
    file_ext="eigenstratpca"

    def __init__( self, **kwd ):
        Rgenetics.__init__(self, **kwd)
        self.add_composite_file( '%s.eigenstratpca', description = 'Eigenstrat PCA file', substitute_name_with_metadata = 'base_name' )


class Snptest(Rgenetics):
    """
    BioC snptest Rgenetics data collections
    """
    file_ext="snptest"


class Pheno(Tabular):
    """
    base class for pheno files
    """
    file_ext = 'pheno'


class RexpBase( Html ):
    """
    base class for BioC data structures in Galaxy 
    must be constructed with the pheno data in place since that
    goes into the metadata for each instance
    """
    MetadataElement( name="columns", default=0, desc="Number of columns",  visible=True )
    MetadataElement( name="column_names", default=[], desc="Column names", visible=True )
    MetadataElement(name="pheCols",default=[],desc="Select list for potentially interesting variables",visible=True)
    MetadataElement( name="base_name", 
    desc="base name for all transformed versions of this expression dataset", default='rexpression', set_in_upload=True)
    MetadataElement( name="pheno_path", desc="Path to phenotype data for this experiment", default="rexpression.pheno", visible=True)
    file_ext = 'rexpbase'
    html_table = None
    is_binary = True
    composite_type = 'auto_primary_file'
    allow_datatype_change = False
    
    
    def __init__( self, **kwd ):
        Html.__init__(self,**kwd)
        self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file', 
          substitute_name_with_metadata = 'base_name', 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
        """
        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'

    def get_mime(self):
        """Returns the mime type of the datatype"""
        return 'text/html'
    
    def get_phecols(self, phenolist=[], maxConc=20):
        """
        sept 2009: cannot use whitespace to split - make a more complex structure here
        and adjust the methods that rely on this structure
        return interesting phenotype column names for an rexpression eset or affybatch
        to use in array subsetting and so on. Returns a data structure for a
        dynamic Galaxy select parameter.
        A column with only 1 value doesn't change, so is not interesting for
        analysis. A column with a different value in every row is equivalent to a unique
        identifier so is also not interesting for anova or limma analysis - both these
        are removed after the concordance (count of unique terms) is constructed for each
        column. Then a complication - each remaining pair of columns is tested for 
        redundancy - if two columns are always paired, then only one is needed :)
        """
        for nrows,row in enumerate(phenolist): # construct concordance
            if len(row.strip()) == 0:
                break
            row = row.strip().split('\t')
            if nrows == 0: # set up from header
               head = row
               totcols = len(row) 
               concordance = [{} for x in head] # list of dicts
            else:
                for col,code in enumerate(row): # keep column order correct
                    if col >= totcols:
                          gal_Log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head))
                    else:
                        concordance[col].setdefault(code,0) # first one is zero
                        concordance[col][code] += 1 
        useCols = []
        useConc = [] # columns of interest to keep
        nrows = len(phenolist)
        nrows -= 1 # drop head from count
        for c,conc in enumerate(concordance): # c is column number
            if (len(conc) > 1) and (len(conc) < min(nrows,maxConc)): # not all same and not all different!!
                useConc.append(conc) # keep concordance
                useCols.append(c) # keep column
        nuse = len(useCols)
        # now to check for pairs of concordant columns - drop one of these.
        delme = []
        p = phenolist[1:] # drop header 
        plist = [x.strip().split('\t') for x in p] # list of lists
        phe = [[x[i] for i in useCols] for x in plist if len(x) >= totcols] # strip unused data 
        for i in range(0,(nuse-1)): # for each interesting column
            for j in range(i+1,nuse):
                kdict = {}
                for row in phe: # row is a list of lists
                    k = '%s%s' % (row[i],row[j]) # composite key
                    kdict[k] = k
                if (len(kdict.keys()) == len(concordance[useCols[j]])): # i and j are always matched
                    delme.append(j)
        delme = list(set(delme)) # remove dupes     
        listCol = [] 
        delme.sort()
        delme.reverse() # must delete from far end!
        for i in delme:
            del useConc[i] # get rid of concordance 
            del useCols[i] # and usecols entry
        for i,conc in enumerate(useConc): # these are all unique columns for the design matrix
                ccounts = [(conc.get(code,0),code) for code in conc.keys()] # decorate
                ccounts.sort()
                cc = [(x[1],x[0]) for x in ccounts] # list of code count tuples
                codeDetails = (head[useCols[i]],cc) # ('foo',[('a',3),('b',11),..])
                listCol.append(codeDetails)
        if len(listCol) > 0:
            res = listCol
            # metadata.pheCols becomes [('bar;22,zot;113','foo'), ...]
        else:
            res = [('no usable phenotype columns found',[('?',0),]),]     
        return res

    

    def get_pheno(self,dataset):
        """
        expects a .pheno file in the extra_files_dir - ugh
        note that R is wierd and adds the row.name in
        the header so the columns are all wrong - unless you tell it not to.
        A file can be written as  
        write.table(file='foo.pheno',pData(foo),sep='\t',quote=F,row.names=F)
        """
        p = file(dataset.metadata.pheno_path,'r').readlines() 
        if len(p) > 0: # should only need to fix an R pheno file once
            head = p[0].strip().split('\t')
            line1 = p[1].strip().split('\t')
            if len(head) < len(line1):
                head.insert(0,'ChipFileName') # fix R write.table b0rken-ness
                p[0] = '\t'.join(head)
        else:
            p = []
        return '\n'.join(p)

    def set_peek( self, dataset, **kwd ):
        """
        expects a .pheno file in the extra_files_dir - ugh
        note that R is wierd and does not include the row.name in
        the header. why?"""
        if not dataset.dataset.purged:
            pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name)
            try:
                p = file(pp,'r').readlines()
            except:
                p = ['##failed to find %s' % pp,]
            dataset.peek = ''.join(p[:5])
            dataset.blurb = 'Galaxy Rexpression composite file'
        else:
            dataset.peek = 'file does not exist\n'
            dataset.blurb = 'file purged from disk'

    def get_peek( self, dataset ):
        """
        expects a .pheno file in the extra_files_dir - ugh
        """
        pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name)
        try:
            p = file(pp,'r').readlines()
        except:
            p = ['##failed to find %s' % pp]
        return ''.join(p[:5])

    def get_file_peek(self,filename):
        """
        can't really peek at a filename - need the extra_files_path and such?
        """
        h = '## rexpression get_file_peek: no file found'
        try:
            h = file(filename,'r').readlines()
        except:
            pass
        return ''.join(h[:5])

    def regenerate_primary_file(self,dataset):
        """
        cannot do this until we are setting metadata 
        """
        bn = dataset.metadata.base_name
        flist = os.listdir(dataset.extra_files_path)
        rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)]
        for i,fname in enumerate(flist):
            sfname = os.path.split(fname)[-1]
            rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) )
        rval.append( '</ul></html>' )
        f = file(dataset.file_name,'w')
        f.write("\n".join( rval ))
        f.write('\n')
        f.close()

    def init_meta( self, dataset, copy_from=None ):
        if copy_from:
            dataset.metadata = copy_from.metadata     

    def set_meta( self, dataset, **kwd ):         

        """
        NOTE we apply the tabular machinary to the phenodata extracted
        from a BioC eSet or affybatch.

        """
        Html.set_meta(self, dataset, **kwd)
        try:
            flist = os.listdir(dataset.extra_files_path)
        except:
            if verbose:
                gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
            return False
        bn = dataset.metadata.base_name
        if not bn:
           for f in flist:
               n = os.path.splitext(f)[0]
               bn = n
               dataset.metadata.base_name = bn
        if not bn:
            bn = '?'
            dataset.metadata.base_name = bn
        pn = '%s.pheno' % (bn)
        pp = os.path.join(dataset.extra_files_path,pn)
        dataset.metadata.pheno_path=pp
        try:
            pf = file(pp,'r').readlines() # read the basename.phenodata in the extra_files_path
        except:
            pf = None
        if pf:
            h = pf[0].strip()
            h = h.split('\t') # hope is header
            h = [escape(x) for x in h]
            dataset.metadata.column_names = h
            dataset.metadata.columns = len(h)
            dataset.peek = ''.join(pf[:5])
        else:
            dataset.metadata.column_names = []
            dataset.metadata.columns = 0
            dataset.peek = 'No pheno file found'
        if pf and len(pf) > 1:
            dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
        else:
            dataset.metadata.pheCols = [('','No useable phenotypes found',False),]
        #self.regenerate_primary_file(dataset)
        if not dataset.info:
                dataset.info = 'Galaxy Expression datatype object'
        if not dataset.blurb:
               dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
        return True
            
    def make_html_table( self, pp='nothing supplied from peek\n'):
        """
        Create HTML table, used for displaying peek
        """
        out = ['<table cellspacing="0" cellpadding="3">',]
        p = pp.split('\n')
        try:
            # Generate column header
            for i,row in enumerate(p):
                lrow = row.strip().split('\t')
                if i == 0:                
                    orow = ['<th>%s</th>' % escape(x) for x in lrow]
                    orow.insert(0,'<tr>')
                    orow.append('</tr>')
                else:            
                    orow = ['<td>%s</td>' % escape(x) for x in lrow]
                    orow.insert(0,'<tr>')
                    orow.append('</tr>')
                out.append(''.join(orow))
            out.append( '</table>' )
            out = "\n".join( out )
        except Exception, exc:
            out = "Can't create html table %s" % str( exc )
        return out
    
    def display_peek( self, dataset ):
        """
        Returns formatted html of peek
        """
        out=self.make_html_table(dataset.peek)
        return out
    
    def get_mime(self):
        """
        Returns the mime type of the datatype
        """
        return 'text/html'
    

class Affybatch( RexpBase ):
    """
    derived class for BioC data structures in Galaxy 
    """

    file_ext = "affybatch"

    def __init__( self, **kwd ):
        RexpBase.__init__(self, **kwd)
        self.add_composite_file( '%s.affybatch', description = 'AffyBatch R object saved to file', 
        substitute_name_with_metadata = 'base_name', is_binary=True )
    
class Eset( RexpBase ):
    """
    derived class for BioC data structures in Galaxy 
    """
    file_ext = "eset"

    def __init__( self, **kwd ):
        RexpBase.__init__(self, **kwd)
        self.add_composite_file( '%s.eset', description = 'ESet R object saved to file', 
        substitute_name_with_metadata = 'base_name', is_binary = True )


class MAlist( RexpBase ):
    """
    derived class for BioC data structures in Galaxy 
    """
    file_ext = "malist"    

    def __init__( self, **kwd ):
        RexpBase.__init__(self, **kwd)
        self.add_composite_file( '%s.malist', description = 'MAlist R object saved to file', 
        substitute_name_with_metadata = 'base_name', is_binary = True )


if __name__ == '__main__':
    import doctest, sys
    doctest.testmod(sys.modules[__name__])