def build_table(args, handle, counts): references = collect_references(args, handle) table = {} for (key, readgroup) in collect_readgroups(args, handle).iteritems(): sample = readgroup["SM"] library = readgroup["LB"] # Exclude counts for reads with no read-groups, if none such were seen if key is None and not args.ignore_readgroups: for reference in references: subtable = counts.get(reference, {}).get(key) if subtable is not None and subtable.has_values(): break else: continue for (reference, size) in references.iteritems(): subtable_key = (args.target_name, sample, library, reference) subtable = create_or_get_subtable(table, subtable_key, size) statistics = counts.get(reference, {}).get(key) if statistics is not None: subtable.add(statistics) return table
def build_table(args, handle, counts): references = collect_references(args, handle) table = {} for (key, readgroup) in collect_readgroups(args, handle).iteritems(): sample = readgroup["SM"] library = readgroup["LB"] # Exclude counts for reads with no read-groups, if none such were seen if key is None and not args.ignore_readgroups: for reference in references: subtable = counts.get(reference, {}).get(key) if subtable is not None and subtable.has_values(): break else: continue for (reference, size) in references.iteritems(): subtable_key = (args.target_name, sample, library, reference) subtable = create_or_get_subtable(table, subtable_key, size) statistics = counts.get(reference, {}).get(key) if statistics is not None: subtable.add(statistics) return table
def build_key_struct(args, handle): structure = collections.defaultdict(set) for readgroup in collect_readgroups(args, handle).itervalues(): lb_key = readgroup["LB"] sm_key = readgroup["SM"] structure[sm_key].add(lb_key) return structure
def build_key_struct(args, handle): structure = collections.defaultdict(set) for readgroup in collect_readgroups(args, handle).itervalues(): lb_key = readgroup["LB"] sm_key = readgroup["SM"] structure[sm_key].add(lb_key) return structure
def build_table(args, handle, counts): table = {} for (key, readgroup) in collect_readgroups(args, handle).iteritems(): sample = readgroup["SM"] library = readgroup["LB"] for (reference, size) in collect_references(args, handle).iteritems(): subtable_key = (args.target_name, sample, library, reference) subtable = create_or_get_subtable(table, subtable_key, size) statistics = counts.get(reference, {}).get(key, {}) for (stat, value) in statistics.iteritems(): subtable[stat] += value return table
def build_rg_to_smlbid_keys(args, handle): """Returns a dictionary which maps a readgroup ID to an index value, as well as a list containing a tuple (samples, library) corresponding to each index. Typically, this list will be shorter than the map of read- groups, as multiple read-groups will map to the same sample / library. """ rg_to_lbsmid = {} lbsm_to_lbsmid = {} lbsmid_to_smlb = [] for (key_rg, readgroup) in collect_readgroups(args, handle).iteritems(): key_sm = readgroup["SM"] key_lb = readgroup["LB"] key_lbsm = (key_sm, key_lb) if key_lbsm not in lbsm_to_lbsmid: lbsm_to_lbsmid[key_lbsm] = len(lbsm_to_lbsmid) lbsmid_to_smlb.append(key_lbsm) rg_to_lbsmid[key_rg] = lbsm_to_lbsmid[key_lbsm] return rg_to_lbsmid, lbsmid_to_smlb
def build_rg_to_smlbid_keys(args, handle): """Returns a dictionary which maps a readgroup ID to an index value, as well as a list containing a tuple (samples, library) corresponding to each index. Typically, this list will be shorter than the map of read- groups, as multiple read-groups will map to the same sample / library. """ rg_to_lbsmid = {} lbsm_to_lbsmid = {} lbsmid_to_smlb = [] for (key_rg, readgroup) in collect_readgroups(args, handle).iteritems(): key_sm = readgroup["SM"] key_lb = readgroup["LB"] key_lbsm = (key_sm, key_lb) if key_lbsm not in lbsm_to_lbsmid: lbsm_to_lbsmid[key_lbsm] = len(lbsm_to_lbsmid) lbsmid_to_smlb.append(key_lbsm) rg_to_lbsmid[key_rg] = lbsm_to_lbsmid[key_lbsm] return rg_to_lbsmid, lbsmid_to_smlb
def build_region_template(args, handle): template = {} for key in collect_readgroups(args, handle): template[key] = dict(READGROUP_TEMPLATE) return template
def build_region_template(args, handle): template = {} for key in collect_readgroups(args, handle): template[key] = ReadGroup() return template
def build_region_template(args, handle): template = {} for key in collect_readgroups(args, handle): template[key] = ReadGroup() return template