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#!/usr/bin/python3
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
import numpy
import time
import TNode
logger = logging.getLogger(__name__)
class TGraph:
def __init__(self, gene_id):
self.node_cache = dict()
self.gene_id = gene_id
def get_node(self, transcript_id, loc_node_id, node_seq):
"""
Instantiates Node objects, and stores them in a graph.
*** use this method for instantiating all Node objects ***
use clear_node_cache() to clear the graph
"""
logger.debug("{}\t{}".format(loc_node_id, node_seq))
if len(node_seq) == 0:
raise RuntimeError("Error, non-zero length node_seq required for parameter")
if loc_node_id in self.node_cache:
node_obj = self.node_cache[ loc_node_id ]
node_obj.add_transcripts(transcript_id)
if node_obj.seq != node_seq:
errmsg = "ERROR: have conflicting node sequences for {} node_id: {}\n".format(self.get_gene_id(),
loc_node_id) + "{}\n vs. \n{}".format(node_obj.seq, node_seq)
logger.critical(errmsg)
raise RuntimeError(errmsg)
else:
return node_obj
else:
# instantiate a new one
node_obj = TNode.TNode(self, transcript_id, loc_node_id, node_seq)
self.node_cache[ loc_node_id ] = node_obj
return node_obj
def get_all_nodes(self):
return list(self.node_cache.values())
def clear_node_cache(self):
"""
clears the graph
"""
self.node_cache.clear()
def clear_touch_settings(self):
"""
clear the touch settings for each of the nodes
"""
for node in self.get_all_nodes():
node.clear_touch()
def add_edges(self, from_nodes_list, to_nodes_list):
for from_node in from_nodes_list:
for to_node in to_nodes_list:
from_node.add_next_node(to_node)
to_node.add_prev_node(from_node)
def prune_edges(self, from_nodes_list, to_nodes_list):
for from_node in from_nodes_list:
for to_node in to_nodes_list:
from_node.remove_next_node(to_node)
to_node.remove_prev_node(from_node)
def prune_node(self, node):
logger.debug("pruning node: {}".format(node))
self.prune_edges(node.get_prev_nodes(), [node])
self.prune_edges([node], node.get_next_nodes())
node.dead = True
self.node_cache.pop(node.get_loc_id())
def retrieve_node(self, node_id):
"""
does not instantiate, only retrieves.
If loc_node_id is not in the graph, returns None
"""
if node_id in self.node_cache:
return self.node_cache[node_id]
else:
return None
def get_gene_id(self):
return self.gene_id
def draw_graph(self, filename):
logger.debug("drawing graph: {}".format(filename))
ofh = open(filename, 'w')
ofh.write("digraph G {\n")
for node_id in self.node_cache:
node = self.node_cache[node_id]
node_seq = node.get_seq()
gene_node_id = node.get_gene_node_id()
next_nodes = node.get_next_nodes()
node_seq_len = len(node_seq)
max_len_show = 50
max_len_show_half = int(max_len_show/2)
if node_seq_len > max_len_show:
node_seq = node_seq[0:max_len_show_half] + "..." + node_seq[(node_seq_len-max_len_show_half):node_seq_len]
ofh.write("{} [label=\"{}:Len{}:T{}:{}\"]\n".format(node.get_id(), gene_node_id, node_seq_len,
node.get_topological_order(), node_seq))
for next_node in next_nodes:
ofh.write("{}->{}\n".format(node.get_id(), next_node.get_id()))
ofh.write("}\n") # close it
ofh.close()
def __repr__(self):
txt = ""
for node in self.get_all_nodes():
txt += node.toString() + "\n"
return txt
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