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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
import Trinity_util
logger = logging.getLogger(__name__)
class Node_path:
"""
Object representation of the connected set of Node objects that represent the reconstructed isoforms graph traversal
Instance members:
transcript_name : (str) name of the isoform
node_obj_list : (list) of Node objects
"""
def __init__(self, tgraph, transcript_name, path_string, sequence):
"""
constructor, instantiates Node_path and builds vertices in the graph
"""
self.transcript_name = transcript_name
self.node_obj_list = list()
node_descr_list = re.findall("\d+:\d+\-\d+", path_string)
# 1st node is special (full kmer prefix included)
first_kmer_flag = False
obj_node_list = list()
for node_descr in node_descr_list:
(loc_node_id, node_coord_range) = node_descr.split(":")
(lend,rend) = node_coord_range.split("-")
lend = int(lend)
rend = int(rend)
if not first_kmer_flag:
first_kmer_flag = True
loc_node_id += 'fst'
# use factory call to instantiate node objects:
node_obj = tgraph.get_node(transcript_name,
loc_node_id, sequence[lend:rend+1]) # coords in path were already zero-based
self.node_obj_list.append(node_obj)
def get_transcript_name(self):
return self.transcript_name
def get_path(self):
return self.node_obj_list
def __repr__(self):
node_str_list = list()
for node in self.node_obj_list:
node_str_list.append(str(node))
path_str = "--".join(node_str_list)
return path_str
@staticmethod
def adjust_for_fst_nodes(tgraph, node_path_list):
"""
fst nodes will have an extra 5' sequence as compared to the corresponding non-fst nodes.
If both the fst and non-fst version of the node exist, must modify the fst nodes so that
they are separated from their 5' extension, and the core of the node (suffix) is shared.
input: TGraph obj, list of node_path objects.
The node_path objects are modified in-place as needed.
A fst-node will be truncated to the unique prefix and the non-fst node will be integrated into the path.
returns the node_path_list with any required adjustments
"""
# get list of fst nodes requiring adjustment
fst_nodes_require_adj = list()
nodes = tgraph.get_all_nodes()
for node in nodes:
node_id = node.get_loc_id()
if re.search("fst", node_id):
core_node_id = re.sub("fst", "", node_id)
core_node = tgraph.retrieve_node(core_node_id)
if core_node is not None:
fst_nodes_require_adj.append( (node, core_node) )
if not fst_nodes_require_adj:
# nothing to do
logger.debug("no FST nodes to adjust")
return node_path_list
logger.debug("Adjusting FST nodes: {}".format(fst_nodes_require_adj))
old_fst_node_to_new_fst_nodes = dict()
fst_nodes_to_delete = list()
# perform node modifications:
for (fst_node, core_node) in fst_nodes_require_adj:
fst_node_seq = fst_node.get_seq()
core_node_seq = core_node.get_seq()
# reverse, index, then revcomp the index value to get the actual position.
fst_node_seq_rev = fst_node_seq[::-1]
core_node_seq_rev = fst_node_seq[::-1]
if not re.match(core_node_seq_rev, fst_node_seq_rev):
raise RuntimeError("Error, core_node_seq:\n{}\nis not a suffix of fst seq:\n{}\n".format(core_node_seq, fst_node_seq))
prefix_endpt = len(fst_node_seq) - len(core_node_seq)
if prefix_endpt == 0:
assert fst_node_seq == core_node_seq, "Error, prefix starts at first position but sequences are not equivalent"
core_node.add_transcripts(fst_node.get_transcripts())
old_fst_node_to_new_fst_nodes[fst_node] = [core_node]
fst_nodes_to_delete.append(fst_node)
else:
prefix_string = fst_node_seq[0:prefix_endpt]
logger.debug("FST-SEQ-EXTRACTION\n\nFSTseq:\n{}\n\nCOREseq:\n{}\n\nPREFIXseq:\n{}\n\n".format(fst_node_seq, core_node_seq, prefix_string))
core_node.add_transcripts(fst_node.get_transcripts())
old_fst_node_to_new_fst_nodes[fst_node] = [fst_node, core_node]
fst_node.set_seq(prefix_string)
# now perform node path updates
for node_path in node_path_list:
nodes = node_path.get_path()
first_node = nodes[0]
if first_node in old_fst_node_to_new_fst_nodes:
# must replace
replacement_node_list = old_fst_node_to_new_fst_nodes[first_node]
if len(replacement_node_list) == 1:
# swap it out
nodes[0] = replacement_node_list[0]
elif len(replacement_node_list) == 2:
nodes[0] = replacement_node_list[1]
nodes.insert(0, replacement_node_list[0])
else:
raise RuntimeError("shouldn't get here")
# purge the nodes targeted for deletion
for node in fst_nodes_to_delete:
tgraph.prune_node(node)
return node_path_list
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