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 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 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 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 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 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 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 loadTranscripts(infile, outfile):
'''load the transcript set.'''
PGeneset.loadTranscripts(infile, outfile)
def loadGeneInformation(infile, outfile):
'''load the transcript set.'''
PGeneset.loadGeneInformation(infile, outfile)
def buildCDNAFasta(infile, outfile):
'''load ENSEMBL peptide file
*infile* is an ENSEMBL .cdna.all.fa.gz file.
'''
PGeneset.buildCDNAFasta(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 loadTranscriptInformation(infile, outfile):
'''load the transcript set.'''
PGeneset.loadTranscriptInformation(
infile,
outfile,
only_proteincoding=PARAMS["ensembl_only_proteincoding"])
def buildPeptideFasta(infile, outfile):
'''load ENSEMBL peptide file
*infile* is an ENSEMBL .pep.all.fa.gz file.
'''
PGeneset.buildPeptideFasta(infile, outfile)
def loadProteinStats(infile, outfile):
'''load the transcript set.'''
PGeneset.loadProteinStats(infile, outfile)
def importTranscriptInformation( infile, outfile ):
'''import the transcript set.'''
PGeneset.importTranscriptInformation( infile, outfile,
only_proteincoding = PARAMS["geneset_only_proteincoding"] )
def importProteinStats( infile, outfile ):
'''import the transcript set.'''
PGeneset.importProteinStats( infile, outfile )
def loadProteinStats(infile, outfile):
'''load the transcript set.'''
PGeneset.loadProteinStats(infile, outfile)
def importTranscripts( infile, outfile ):
'''import the transcript set.'''
PGeneset.importTranscripts( infile, outfile )
