def extractLncRNAFastaAlignments(infiles, outfile): """ Recieves a MAF file containing pairwise alignments and a gtf12 file containing intervals. Outputs a single fasta file containing aligned sequence for each interval. """ bed_file, maf_file = infiles maf_tmp = P.getTempFilename("./phyloCSF") to_cluster = False statement = ("gunzip -c %(maf_file)s > %(maf_tmp)s") P.run() target_genome = PARAMS["genome"] query_genome = PARAMS["phyloCSF_query_genome"] genome_file = os.path.join(PARAMS["genomedir"], PARAMS["genome"]) gene_models = PipelineLncRNA.extractMAFGeneBlocks(bed_file, maf_tmp, genome_file, outfile, target_genome, query_genome, keep_gaps=False) E.info("%i gene_models extracted" % gene_models) os.unlink(maf_tmp)
def extractControllLncRNAFastaAlignments(infiles, outfile): bed_file, maf_file = infiles maf_tmp = P.getTempFilename("/ifs/scratch") to_cluster = False statement = ("gunzip -c %(maf_file)s > %(maf_tmp)s") P.run() target_genome = PARAMS["genome"] query_genome = PARAMS["phyloCSF_query_genome"] genome_file = os.path.join(PARAMS["genomedir"], PARAMS["genome"]) gene_models = PipelineLncRNA.extractMAFGeneBlocks(bed_file, maf_tmp, genome_file, outfile, target_genome, query_genome, keep_gaps=False) E.info("%i gene_models extracted" % gene_models) os.unlink(maf_tmp)