import sys
import json
sys.path.append("../lib")
import odgi
# invoke with $python3 jsoner.py [file name without suffix]
file_name = sys.argv[1]
json_file = open(file_name + ".json")
dat = json.load(json_file)
gr = odgi.graph()
handles = dict()
for node in dat['node']:
id = node['id']
seq = node['sequence']
handles[id] = gr.create_handle(seq)
for edge in dat['edge']:
fr = edge['from']
to = edge['to']
gr.create_edge(handles[fr], handles[to])
for path in dat['path']:
name = path['name']
path['mapping'].sort(key=lambda x: x['rank'])
path_handle = gr.create_path_handle(name)
for mapping in path['mapping']:
id = mapping['position']['node_id']
gr.append_step(path_handle, handles[id])
import sys
sys.path.append('/home/flavia/Lab/odgi/lib')
import odgi
g = odgi.graph()
g.load("/home/flavia/Desktop/gfa2vcf/q3.odgi")
def process_step(s):
h = g.get_handle_of_step(s) # gets the handle (both node and orientation) of the step
is_rev = g.get_is_reverse(h)
id = g.get_id(h)
return str(id) + ("+" if not is_rev else "-")
path_to_steps_dict = {}
def create_into_dict(path, step): #dizionario nodo id come chiave e come valore un altro dizionario che ha come chiave il nome del path
path_name = g.get_path_name(path)
if path_name not in path_to_steps_dict:
path_to_steps_dict[path_name] = []
path_to_steps_dict[path_name].append(process_step(step))
g.for_each_path_handle(
lambda p:
g.for_each_step_in_path(p, lambda s: create_into_dict(p, s))
)
node_id_to_path_and_pos_dict = {}
for path_name, steps_list in path_to_steps_dict.items():
#print(path_name)
pos = 0
for nodeId_isRev in steps_list:
def open(self, odgi_file, create=False):
og = odgi.graph()
ogf = og.load(odgi_file)
self.odgi_graph = og
self.odgi_graph.for_each_path_handle(
CollectPaths(self.knownPaths, self.odgi_graph, self.base))
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# this shows some examples of how to use the python bindings to odgi
import sys
if len(sys.argv) is 1:
print("usage: PYTHONPATH=../lib", sys.argv[0], "graph.og")
print("displays information about the graph, and iterates over it")
print(
"to build the input graph, use `odgi build -g graph.gfa -o graph.og`")
exit(1)
import odgi
g = odgi.graph()
g.load(sys.argv[1])
# the number of nodes and edges is given
print("node count:", g.get_node_count())
print("path count:", g.get_path_count())
# iterate over the nodes and sum the sequence length
# we have to use a counter object to count
# because in python you can't assign inside lambdas 🤦
# and there are no true closures over local variables ðŸ˜
class counter:
total = 0
def add(self, l):
def open(self, odgifile, create=False):
og = odgi.graph()
ogf = og.load(odgifile)
self.odgi = og
