def flagExonStatus(infile, outfile): ''' Adds two attributes to the gtf entry: exon_status_locus - specifies whether the gene model is multi- or single exon exon_status - specifies whether the transcript is mult- or single exon ''' PipelineLncRNA.flagExonStatus(infile, outfile)
def buildRefcodingGeneSetStats(infile, outfile): ''' counts: no. of transcripts no. genes average number of exons per transcript average number of exons per gene no. multi-exon transcripts no. single exon transcripts no. multi-exon genes no. single exon genes in the coding and lncRNA genesets ''' # calculate exon status for refcoding genes. tmpf = P.getTempFilename(".") + ".gz" PipelineLncRNA.flagExonStatus(infile, tmpf) outf = open(outfile, "w") outf.write("\t".join(["no_transcripts", "no_genes", "no_exons_per_transcript", "no_exons_per_gene", "no_single_exon_transcripts", "no_multi_exon_transcripts", "no_single_exon_genes", "no_multi_exon_genes"]) + "\n") outf.write("\t".join(map(str, [PipelineLncRNA.CounterTranscripts(tmpf).count(), PipelineLncRNA.CounterGenes(tmpf).count(), PipelineLncRNA.CounterExonsPerTranscript(tmpf).count(), PipelineLncRNA.CounterExonsPerGene(tmpf).count(), PipelineLncRNA.CounterSingleExonTranscripts(tmpf).count(), PipelineLncRNA.CounterMultiExonTranscripts(tmpf).count(), PipelineLncRNA.CounterSingleExonGenes(tmpf).count(), PipelineLncRNA.CounterMultiExonGenes(tmpf).count()]))) os.unlink(tmpf) os.unlink(tmpf + ".log") os.unlink(P.snip(tmpf, ".gz"))
def buildRefcodingGeneSetStats(infile, outfile): ''' counts: no. of transcripts no. genes average number of exons per transcript average number of exons per gene no. multi-exon transcripts no. single exon transcripts no. multi-exon genes no. single exon genes in the coding and lncRNA genesets ''' # calculate exon status for refcoding genes. tmpf = P.getTempFilename(".") + ".gz" PipelineLncRNA.flagExonStatus(infile, tmpf) outf = IOTools.openFile(outfile, "w") outf.write("\t".join([ "no_transcripts", "no_genes", "no_exons_per_transcript", "no_exons_per_gene", "no_single_exon_transcripts", "no_multi_exon_transcripts", "no_single_exon_genes", "no_multi_exon_genes" ]) + "\n") outf.write("\t".join( map(str, [ PipelineLncRNA.CounterTranscripts(tmpf).count(), PipelineLncRNA.CounterGenes(tmpf).count(), PipelineLncRNA.CounterExonsPerTranscript(tmpf).count(), PipelineLncRNA.CounterExonsPerGene(tmpf).count(), PipelineLncRNA.CounterSingleExonTranscripts(tmpf).count(), PipelineLncRNA.CounterMultiExonTranscripts(tmpf).count(), PipelineLncRNA.CounterSingleExonGenes(tmpf).count(), PipelineLncRNA.CounterMultiExonGenes(tmpf).count() ]))) os.unlink(tmpf) os.unlink(tmpf + ".log") os.unlink(P.snip(tmpf, ".gz"))
def flagExonStatus(infile, outfile): """ Adds an attribute to the gtf entry dependent on whether the lncRNA is multi or single exon """ PipelineLncRNA.flagExonStatus(infile, outfile)
def flagExonStatus(infile, outfile): ''' Adds an attribute to the gtf entry dependent on whether the lncRNA is multi or single exon ''' PipelineLncRNA.flagExonStatus(infile, outfile)