def prepare_overlap(genome): """Converts indexing info into a dictionary""" package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3]) genome_dir = package_dir + '/annotations/' + genome if os.path.isdir(genome_dir): est_file = genome_dir + '/' + 'all_est.txt' index_file = est_file + '.idx' est_overlap = OverlapCoord(est_file, index_file) est_overlap.extract_index() return est_overlap return None
def prepare_overlap(genome, annodir): """Converts indexing info into a dictionary""" genome_dir = os.path.join(annodir, genome) if os.path.isdir(genome_dir): est_file = genome_dir + '/' + 'all_est.txt' index_file = est_file + '.idx' est_overlap = OverlapCoord(est_file, index_file) est_overlap.extract_index() return est_overlap return None
def prepare_overlap(genome, chrom): """Extracts index info into dictionary""" package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3]) genome_dir = package_dir + '/annotations/' + genome if not os.path.isdir(genome_dir): return None snp_file = genome_dir + '/snp/' + chrom + '-snp.txt' index_file = snp_file + '.idx' if not os.path.exists(snp_file) or not os.path.exists(index_file): return None snp_overlap = OverlapCoord(snp_file, index_file) snp_overlap.extract_index() return snp_overlap
def prepare_overlap(genome, chrom, annodir): """Extracts index info into dictionary""" genome_dir = os.path.join(annodir, genome) if not os.path.isdir(genome_dir): return None snp_file = genome_dir + "/snp/" + chrom + "-snp.txt" index_file = snp_file + ".idx" if not os.path.exists(snp_file) or not os.path.exists(index_file): return None snp_overlap = OverlapCoord(snp_file, index_file) snp_overlap.extract_index() return snp_overlap
def prepare_overlap(genome, annodir): """Extracts index info into dictionary""" genome_dir = os.path.join(annodir, genome) if not os.path.isdir(genome_dir): return None dgv_file = genome_dir + '/dgv.txt' index_file = genome_dir + '/dgv.idx' if not os.path.exists(dgv_file) or not os.path.exists(index_file): return None dgv_overlap = OverlapCoord(dgv_file, index_file) dgv_overlap.extract_index() return dgv_overlap
def prepare_overlap(genome): """Extracts index info into dictionary""" package_dir = "/".join(os.path.abspath(__file__).split("/")[:-3]) genome_dir = package_dir + '/annotations/' + genome if not os.path.isdir(genome_dir): return None dgv_file = genome_dir + '/dgv.txt' index_file = genome_dir + '/dgv.idx' if not os.path.exists(dgv_file) or not os.path.exists(index_file): return None dgv_overlap = OverlapCoord(dgv_file, index_file) dgv_overlap.extract_index() return dgv_overlap
def prepare_overlap(cls, genome, models): """Prepares transcript overlapping for given genome and models""" overlaps = {} config = ConfigParser.ConfigParser() config.read(PACKAGE_DIR + "/configs/model_matcher.cfg") for m in models.split(','): config = ConfigParser.ConfigParser() config.read(PACKAGE_DIR + "/configs/model_matcher.cfg") annot_file = index = None if genome in config.sections(): for field in config.options(genome): if field.lower() == m.lower(): annot_file = PACKAGE_DIR + "/annotations/" + genome + "/" + config.get(genome, field) if annot_file and os.path.exists(annot_file): index_file = annot_file.replace('.txt', '.idx') txt_overlap = OverlapCoord(annot_file, index_file) txt_overlap.extract_index() overlaps[m] = txt_overlap return overlaps
def prepare_overlap(cls, genome, models, annodir, mmcfg): """Prepares transcript overlapping for given genome and models""" overlaps = {} config = ConfigParser.ConfigParser() config.read(mmcfg) for m in models.split(','): config = ConfigParser.ConfigParser() config.read(mmcfg) annot_file = index = None if genome in config.sections(): for field in config.options(genome): if field.lower() == m.lower(): annot_file = os.path.join(annodir, genome, config.get(genome, field)) if annot_file and os.path.exists(annot_file): index_file = annot_file.replace('.txt', '.idx') txt_overlap = OverlapCoord(annot_file, index_file) txt_overlap.extract_index() overlaps[m] = txt_overlap return overlaps