def parse(tab_file, anno_id, genome_id, db_name, tab_type):
entries = {}
file_handler_2 = open(tab_file, "r")
entry = None
for line in file_handler_2:
values = line.split()
if tab_type[0] == str(values[1]):
entry = {}
start = int(values[3])
stop = int(values[4])
seq_id = values[2]
strand = "+"
name = values[0]
if start >= stop:
h = start
start = stop
stop = h
strand = "-"
start = str(start)
stop = str(stop)
entry["seq_lower_coor"] = start
entry["seq_upper_coor"] = stop
entry["name"] = name
entry["seq_id"] = seq_id
entry["freq_coor"] = start + ";" + stop
entry["strand"] = strand
entries[entry["name"]] = entry
if len(entries) > 0:
sqlite_methods.saveGFFTypeElementsInDb(entries, db_name, genome_id, anno_id, "")
def parse_gff(gff3_file, db_name, allowed_gff3_types, genome_id, anno_id, anno_id_overwrite): #, min_chromosome_length):
try:
#min_chromosome_length = check_min_chromosome_length_db(db_name, genome_id, min_chromosome_length)
dic_indexes_parents = {}
nodes_line_indexes = {}
gff3_types = getGFF3Types(gff3_file)
gff3_relation_map = getGFF3TypesHierarchy(gff3_file, gff3_types)
for key in gff3_relation_map.keys():
gff3_relation_map[key] = gff3_relation_map[key].keys()
hierarchy = {}
for allowed_gff3_type1 in allowed_gff3_types:
for allowed_gff3_type2 in allowed_gff3_types:
paths = find_all_paths(gff3_relation_map, allowed_gff3_type1, allowed_gff3_type2)
for path in paths:
path_possible = True
for allowed_gff3_type3 in allowed_gff3_types:
try:
(path.index(allowed_gff3_type3) == -1)
except Exception:
path_possible = False
if(path_possible):
level = 0
for node in path:
level = level + 1
if(hierarchy.get(level) == None):
hierarchy[level] = {}
hierarchy[level][node] = 1
assert(len(paths[0]) == len(path))
gff3_children = hierarchy.get(len(hierarchy))
gff3_parents = hierarchy.get(len(hierarchy) - 1)
index_list_parents_parents_allowed = extractElementsToRemove(gff3_file, hierarchy)
index_list_parents = extractElements(gff3_file, gff3_parents, index_list_parents_parents_allowed)
index_list_parents = extractFragments(gff3_file, gff3_children, index_list_parents)
sqlite_methods.saveGFFTypeElementsInDb(index_list_parents, db_name, genome_id, anno_id, anno_id_overwrite)
except Exception:
print "ERROR", "parse_gff", sys.exc_info()
def parse(tab_file, anno_id, genome_id, db_name, tab_type):
entries = {}
file_handler_2 = open(tab_file, "r")
entry = None
for line in file_handler_2:
values = line.split()
if (tab_type[0] == str(values[1])):
entry = {}
start = int(values[3])
stop = int(values[4])
seq_id = values[2]
strand = "+"
name = values[0]
if (start >= stop):
h = start
start = stop
stop = h
strand = "-"
start = str(start)
stop = str(stop)
entry["seq_lower_coor"] = start
entry["seq_upper_coor"] = stop
entry["name"] = name
entry["seq_id"] = seq_id
entry["freq_coor"] = start + ";" + stop
entry["strand"] = strand
entries[entry["name"]] = entry
if (len(entries) > 0):
sqlite_methods.saveGFFTypeElementsInDb(entries, db_name, genome_id,
anno_id, "")