def buildLincRNAExonTranscript(infile, outfile): ''' Output of the lincRNA features from an ENSEMBL gene set Takes all of the features from a :term:`gtf` file that are features of ``lincRNA`` Arguments --------- infile : from ruffus ENSEMBL geneset, filename named in pipeline.yml outfile : from ruffus Output filename named in pipeline.yml filteroption : string Filter option set in the piepline.yml as feature column in GTF nomenclature ''' m = gtfsubset.SubsetGTF(infile) filteroptions = [ PARAMS['ensembl_cgat_feature'], PARAMS['ensembl_cgat_gene_biotype'] ] filteritem = ["exon", "lincRNA"] m.filterGTF(outfile, filteroptions, filteritem, operators="and")
def buildNonCodingExonTranscript(infile, outfile): ''' Output of the non-coding exon features from an ENSEMBL gene set Remove all of the features from a :term:`gtf` file that are features of ``exon`` and are protein-coding Arguments --------- infile : from ruffus ENSEMBL geneset, filename named in pipeline.yml outfile : from ruffus Output filename named in pipeline.yml filteroption : string Filter option set in the piepline.yml as feature column in GTF nomenclature ''' m = gtfsubset.SubsetGTF(infile) filteroptions = [ PARAMS['ensembl_cgat_feature'], PARAMS['ensembl_cgat_gene_biotype'] ] filteritem = ["exon", "protein_coding"] m.filterGTF(outfile, filteroptions, filteritem, operators="and not")
def buildCdsTranscript(infile, outfile): ''' Output the CDS features from an ENSEMBL gene set takes all of the features from a :term:`gtf` file that are feature types of ``CDS``. Note - we have not filtered on gene_biotype because some of the CDS are classified as polymorphic_pseudogene. Arguments --------- infile : from ruffus ENSEMBL geneset, filename named in pipeline.yml outfile : from ruffus Output filename named in pipeline.yml filteroption : string Filter option set in the piepline.yml as feature column in GTF nomenclature ''' m = gtfsubset.SubsetGTF(infile) filteroption = PARAMS['ensembl_cgat_feature'] filteritem = ["CDS"] m.filterGTF(outfile, filteroption, filteritem, operators=None)