Python PipelineGeneset類代碼示例

def buildTranscripts(infile, outfile):
    '''build a collection of transcripts from the protein-coding
    section of the ENSEMBL gene set.

    Only CDS are used.
    '''
    PGeneset.buildProteinCodingTranscripts(infile, outfile)

def buildCDSFasta(infile, outfile):
    '''build cds sequences from peptide and cds file.

    *infile* is an ENSEMBL .cdna.all.fa.gz file.
    '''

    PGeneset.buildCDSFasta(infile, outfile)

def buildGeneRegions(infile, outfile):
    '''annotate genomic regions with reference gene set.

    Only considers protein coding genes. In case of overlapping
    genes, only take the longest (in genomic coordinates).
    Genes not on UCSC contigs are removed.
    '''
    PGeneset.buildGeneRegions(infile, outfile)

def buildGenes(infile, outfile):
    '''build a collection of exons from the protein-coding
    section of the ENSEMBL gene set. The exons include both CDS
    and UTR.

    The set is filtered in the same way as in :meth:`buildGeneRegions`.
    '''
    PGeneset.buildProteinCodingGenes(infile, outfile)

def loadProteinStats(infile, outfile):
    '''load the transcript set.'''

    PGeneset.loadProteinStats(infile, outfile)

def buildCDNAFasta(infile, outfile):
    '''load ENSEMBL peptide file

    *infile* is an ENSEMBL .cdna.all.fa.gz file.
    '''
    PGeneset.buildCDNAFasta(infile, outfile)

def buildPeptideFasta(infile, outfile):
    '''load ENSEMBL peptide file

    *infile* is an ENSEMBL .pep.all.fa.gz file.
    '''
    PGeneset.buildPeptideFasta(infile, outfile)

def loadTranscriptInformation(infile, outfile):
    '''load the transcript set.'''
    PGeneset.loadTranscriptInformation(infile,
                                       outfile,
                                       only_proteincoding=PARAMS["ensembl_only_proteincoding"])

def loadTranscripts(infile, outfile):
    '''load the transcript set.'''
    PGeneset.loadTranscripts(infile, outfile)

def loadGeneInformation(infile, outfile):
    '''load the transcript set.'''
    PGeneset.loadGeneInformation(infile, outfile)

def importProteinStats( infile, outfile ):
    '''import the transcript set.'''

    PGeneset.importProteinStats( infile, outfile )

def importTranscriptInformation( infile, outfile ):
    '''import the transcript set.'''
    PGeneset.importTranscriptInformation( infile, outfile,
                                          only_proteincoding = PARAMS["geneset_only_proteincoding"] )

def importTranscripts( infile, outfile ):
    '''import the transcript set.'''
    PGeneset.importTranscripts( infile, outfile )