This is a Python module containing methods used in the GCB web-application. Contains classes and methods used to create and process the graph representation of a genomes set.
This module describes the main object GenomeGraph.
| attribute | type | description |
|---|---|---|
dict_graph |
dict |
a dictionary form of graph representation |
dict_graph_freq |
dict |
a dictionary form of graph represenration with frequncy for each edge |
list_graph |
dict |
structure which store sequnces of nodes for each contig. Access to elements is by genome code and contig code |
genes_code |
dict |
table which bind real name of orthology group and its code (real name is key, code is value) |
genes_decode |
dict |
table which bind code of orthology group and its real name (code is key, real name is value) |
| method | description | return |
|---|---|---|
read_graph (file=None, names_list='all', generate_freq=False) |
Reads a sif file and creates a graph structure | no returned value |
compute_complexity (outdir, reference, window=20, iterations=500, min_depth=0, max_depth=-1, save_db=None) |
Computes all types of complexity with the full-graph approach | no returned value |
compute_subgraph_complexity (outdir, reference, window=20, iterations=500, min_depth=0, max_depth=-1, save_db=None) |
Computes all types of complexity with the subgraph approach | no returned value |
generate_subgraph (self, start_node, end_node, reference, window=20, tails=0, depth=-1, minimal_edge=1) |
Generates subgraph with user-dfined parameters | subgraph |
find_paths (start, main_chain, min_depth=0, max_depth=-1, window=20) |
Returns deviating paths set generated by "by genomes" method | list of paths |
find_probabilistic_paths (start, main_chain, iterations=500, min_depth=0, max_depth=-1, window=20) |
Returns deviating paths set generated by probabilistic method | list of paths |
find_template (template, method='st', ref='default') |
Find user-defined template in graph structure | template hits list |
find_local_paths (subgr, start, main_chain, window=20) |
Returns deviating paths set in subgraph generated by "by genomes" method | list of paths |
find_local_probabilistic_paths (subgr, start, main_chain, iterations=500, min_depth=0, max_depth=-1, window=20) |
Returns deviating paths set in subgraph generated by probabilistic method | list of paths |
save_to_db (self, data, out_db, contig, stamm, window=20) |
Saves complexity data to database | no returned value |
save_data (self, data, outdir, contig) |
Saves compelxity data in txt format | no returned value |