Python images.Html类代码示例

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

        """
        for lped/pbed eg

        """
        Html.set_meta( self, dataset, **kwd )
        if kwd.get('overwrite') == False:
            return True
        try:
            efp = dataset.extra_files_path
        except: 
            return False
        try:
            flist = os.listdir(efp)
        except:
            return False
        if len(flist) == 0:
            return False
        self.regenerate_primary_file(dataset)
        if not dataset.info:           
                dataset.info = 'Galaxy Impute2 datatype object'
        if not dataset.blurb:
               dataset.blurb = 'Composite file - Otago Impute2 Galaxy toolkit'
        return True

    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

 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 __init__( self, **kwd ):
        Html.__init__( self, **kwd )

        log.debug("#########  FUSION INSPECTOR DATA ############\n\n\n")
        #sys.exit(1)

        self.add_composite_file('FInspector.fusion_predictions.txt', description = 'fusion predictions',  is_binary = False )

        self.add_composite_file('FInspector.fa', description = 'fusion contigs', mimetype = 'text/html', is_binary = False )
        self.add_composite_file('FInspector.fa.fai', description = 'fusion contigs index', is_binary = False )
        self.add_composite_file("FInspector.fusion_predictions.txt", description="fusion predictions summary", is_binary=False)
        self.add_composite_file("FInspector.igv.FusionJuncSpan", description="fusion support for IGV viewing", is_binary=False)
        self.add_composite_file("FInspector.consolidated.cSorted.bam", description="all fusion-supporting reads", is_binary=True)
        self.add_composite_file("FInspector.consolidated.cSorted.bam.bai", description="bam index", is_binary=True)
        self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz", description="junction reads in bed.gz format", is_binary=True)
        self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for junction reads bed.gz", is_binary=True)
        self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz", description="spanning reads in bed.gz format", is_binary=True)
        self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for spanning reads bed.gz", is_binary=True)
        self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz", description="Trinity fusion transcript structures", is_binary=True)
        self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz.tbi", description="tabix index for trinity fusion transcript structures in bed.gz", is_binary=True)

 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 __init__(self, **kwd):
     Html.__init__(self, **kwd)
     self.add_composite_file(
         "Sequences",
         mimetype="text/html",
         description="Sequences",
         substitute_name_with_metadata=None,
         is_binary=False,
     )
     self.add_composite_file(
         "Roadmaps",
         mimetype="text/html",
         description="Roadmaps",
         substitute_name_with_metadata=None,
         is_binary=False,
     )
     self.add_composite_file(
         "Log",
         mimetype="text/html",
         description="Log",
         optional="True",
         substitute_name_with_metadata=None,
         is_binary=False,
     )

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

 def __init__( self, **kwd ):
     Html.__init__( self, **kwd )
     self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False )
     self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False )
     self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=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 set_meta( self, dataset, **kwd ):
     log.debug("## set_meta for FusionInspector ")
     Html.set_meta( self, dataset, **kwd )
     self.regenerate_primary_file(dataset)

 def __init__(self, **kwd):
     Html.__init__(self, **kwd)

 def __init__( self, **kwd ):
     Html.__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 )