def extract_monocluster_ids(self,
clusters_dict,
white_list_ids=None,
out_file=None):
"""
Extracts clusters with only one sequence in all species.
"""
monocluster_ids = IdSet()
cluster_names = self.get_cluster_names(clusters_dict)
for cluster_name in cluster_names:
for species in clusters_dict:
if white_list_ids:
if cluster_name not in white_list_ids:
break
if cluster_name not in clusters_dict[species]:
break
if len(clusters_dict[species][cluster_name]) > 1:
break
else:
monocluster_ids.add(cluster_name)
if out_file:
monocluster_ids.write(out_file)
return monocluster_ids
def convert_rm_out_to_gff(input_file, output_file, annotated_repeat_classes_file, annotated_repeat_families_file):
repeat_classes_set = IdSet()
repeat_families_set = IdSet()
with open(input_file, "r") as in_fd:
for i in range(0, 3):
in_fd.readline()
with open(output_file, "w") as out_fd:
for line in in_fd:
tmp = line.strip().split()
strand = "+" if tmp[8] == "+" else "-"
repeat_class_family = tmp[10].split("/")
if len(repeat_class_family) == 1:
repeat_class_family.append(".")
repeat_classes_set.add(repeat_class_family[0])
repeat_families_set.add("/".join(repeat_class_family))
parameters = "Class=%s;Family=%s;Matching_repeat=%s;SW_score=%s;Perc_div=%s;Perc_del=%s;Pers_ins=%s" \
% (repeat_class_family[0], repeat_class_family[1],
tmp[9], tmp[0], tmp[1], tmp[2], tmp[3])
out_fd.write("%s\tRepeatMasker\trepeat\t%s\t%s\t.\t%s\t.\t%s\n" % (tmp[4], tmp[5], tmp[6], strand, parameters))
repeat_classes_set.write(annotated_repeat_classes_file)
repeat_families_set.write(annotated_repeat_families_file)