def classifyLncRNA(infiles, outfile): ''' Classify lncRNA realtive to protein coding loci Classify lincRNA in terms of their relationship to protein coding genes - creates indices for intervals on the fly - mayb should be creating additional annotations: antisense transcript overlapping protein coding exons on opposite strand antisense_upstream transcript < 2kb from tss on opposite strand antisense_downstream transcript < 2kb from gene end on opposite strand sense_upstream transcript < 2kb from tss on same strand sense_downstream transcript < 2kb from gene end on same strand intergenic transcript >2kb from any protein coding gene intronic overlaps protein coding gene intron on same strand antisense_intronic overlaps protein coding intron on opposite strand ''' PipelineLncRNA.classifyLncRNAGenes( infiles[0], infiles[1], outfile, dist=PARAMS["lncrna_dist"])
def classifyLncRNA(infiles, outfile): ''' Classify lncRNA realtive to protein coding loci Classify lincRNA in terms of their relationship to protein coding genes - creates indices for intervals on the fly - mayb should be creating additional annotations: antisense transcript overlapping protein coding exons on opposite strand antisense_upstream transcript < 2kb from tss on opposite strand antisense_downstream transcript < 2kb from gene end on opposite strand sense_upstream transcript < 2kb from tss on same strand sense_downstream transcript < 2kb from gene end on same strand intergenic transcript >2kb from any protein coding gene intronic overlaps protein coding gene intron on same strand antisense_intronic overlaps protein coding intron on opposite strand ''' PipelineLncRNA.classifyLncRNAGenes(infiles[0], infiles[1], outfile, dist=PARAMS["lncrna_dist"])
def classifyFilteredLncRNA(infiles, outfile): ''' classifies all lincRNA before cpc filtering to define any classes that are represented in the coding set that are filtered NOTE: This task is not included when running the full pipeline ''' PipelineLncRNA.classifyLncRNAGenes( infiles[0], infiles[1], outfile, dist=PARAMS["lncrna_dist"])
def classifyFilteredLncRNA(infiles, outfile): ''' classifies all lincRNA before cpc filtering to define any classes that are represented in the coding set that are filtered ''' PipelineLncRNA.classifyLncRNAGenes(infiles[0], infiles[1], outfile, dist=PARAMS["lncrna_dist"])
def classifyFilteredLncRNA(infiles, outfile): """ classifies all lincRNA before cpc filtering to define any classes that are represented in the coding set that are filtered """ PipelineLncRNA.classifyLncRNAGenes(infiles[0], infiles[1], outfile, dist=PARAMS["lncrna_dist"])