Source code for PopPUNK.web

from re import I
import h5py
import os
import sys
import numpy as np
import pandas as pd
import graph_tool.all as gt
import requests
import networkx as nx
from networkx.readwrite import json_graph

import json

[docs] def sketch_to_hdf5(sketches_dict, output): """Convert dict of JSON sketches to query hdf5 database""" qNames = [] queryDB = h5py.File(os.path.join(output, os.path.basename(output) + '.h5'), 'w') sketches = queryDB.create_group("sketches") for top_key, top_value in sketches_dict.items(): qNames.append(top_key) kmers = [] dists = [] if type(top_value) == str: sketch_dict = json.loads(top_value) else: sketch_dict = top_value sketch_props = sketches.create_group(top_key) for key, value in sketch_dict.items(): try: kmers.append(int(key)) dists.append(np.array(value, dtype='uint64')) except (TypeError, ValueError): if key == "version": sketches.attrs['sketch_version'] = value elif key == "codon_phased": sketches.attrs['codon_phased'] = value elif key == "densified": pass elif key == "bases": sketch_props.attrs['base_freq'] = value elif key == "bbits": sketch_props.attrs['bbits'] = value elif key == "length": sketch_props.attrs['length'] = value elif key == "missing_bases": sketch_props.attrs['missing_bases'] = value elif key == "sketchsize64": sketch_props.attrs['sketchsize64'] = value elif key == "species": pass else: sys.stderr.write(key + " not recognised") sketch_props.attrs['kmers'] = kmers for k_index in range(len(kmers)): k_spec = sketch_props.create_dataset(str(kmers[k_index]), data=dists[k_index], dtype='uint64') k_spec.attrs['kmer-size'] = kmers[k_index] queryDB.close() return qNames
[docs] def graphml_to_json(network_dir): """Converts full GraphML file to JSON subgraph""" labels = [] nodes_list = [] edges_list = [] full_graph = gt.load_graph(os.path.join(network_dir, os.path.basename(network_dir) + "_cytoscape.graphml")) components = gt.label_components(full_graph)[0].a subgraph = gt.GraphView(full_graph, vfilt=(components == components[-1])) subgraph = gt.Graph(subgraph, prune=True),"subgraph.graphml")) G = nx.read_graphml(os.path.join(network_dir,"subgraph.graphml")) for value in G.nodes.values(): labels.append(value['id']) data = json_graph.node_link_data(G) for k,v in data.items(): if k == "nodes": for node in range(len(v)): node_attr = v[node] node_attr['label'] = labels[node] nodes_list.append({'data':node_attr}) elif k == "links": for edge in range(len(v)): edge_attr = v[edge] edges_list.append({'data':edge_attr}) network_dict = {'elements':{'nodes':nodes_list, 'edges':edges_list}} return network_dict
[docs] def highlight_cluster(query, cluster): """Colour assigned cluster in Microreact output""" if str(cluster) == str(query): colour = "red" else: colour = "blue" return colour
# TODO: update to new microreact API
[docs] def api(query, ref_db): """Post cluster and tree information to microreact""" url = "" microreactDF = pd.read_csv(os.path.join(ref_db, os.path.basename(ref_db) + "_microreact_clusters.csv")) microreactDF["Cluster__autocolour"] = microreactDF['Cluster_Cluster__autocolour'] microreactDF["Highlight_Query__colour"] = microreactDF.apply(lambda row: highlight_cluster(query, row["Cluster__autocolour"]), axis = 1) microreactDF = microreactDF.drop(columns=['Cluster_Cluster__autocolour']) clusters = microreactDF.to_csv() with open(os.path.join(ref_db, os.path.basename(ref_db) + ".nwk"), "r") as nwk: tree = description = "A tree representing all samples in the reference database, excluding the query sequence but highlighting its assigned cluster. The cluster assigned to the query is coloured red. If no clusters are highlighted red, query sequence was assigned to a new cluster." data = {"name":"PopPUNK-web","description": description,"data":clusters,"tree":tree} urlResponse =, data = data) microreactResponse = json.loads(urlResponse.text) for key, value in microreactResponse.items(): if key == "url": url = value return url
[docs] def calc_prevalence(cluster, cluster_list, num_samples): """Cluster prevalences for Plotly.js""" clusterCount = cluster_list.count(cluster) prevalence = round(clusterCount / num_samples * 100, 2) return prevalence
def get_aliases(aliasDF, clusterLabels, species): if species == 'Streptococcus pneumoniae': GPS_name = 'unrecognised' for label in clusterLabels: if label in list(aliasDF['sample']): index = list(aliasDF['sample']).index(label) GPS_name = aliasDF['GPSC'][index] alias_dict = {"GPSC":str(GPS_name)} return alias_dict
[docs] def summarise_clusters(output, species, species_db, qNames): """Retreieve assigned query and all cluster prevalences. Write list of all isolates in cluster for tree subsetting""" totalDF = pd.read_csv(os.path.join(output, os.path.basename(output) + "_clusters.csv")) queryDF = totalDF[totalDF['Taxon'].isin(qNames)] queryDF = queryDF.reset_index(drop=True) queries_names = list(queryDF["Taxon"]) queries_clusters = list(queryDF["Cluster"]) num_samples = len(totalDF["Taxon"]) totalDF["Cluster"] = totalDF["Cluster"].astype(str) cluster_list = list(totalDF["Cluster"]) totalDF["Prevalence"] = totalDF.apply(lambda row: calc_prevalence(row["Cluster"], cluster_list, num_samples), axis = 1) totalDF = totalDF.sort_values(by='Prevalence', ascending=False) uniquetotalDF = totalDF.drop_duplicates(subset=['Cluster']) clusters = list(uniquetotalDF['Cluster']) prevalences = list(uniquetotalDF["Prevalence"]) queries_prevalence = [] for query in queries_clusters: queries_prevalence.append(prevalences[clusters.index(str(query))]) # write list of all isolates in cluster clusterDF = totalDF.loc[totalDF['Cluster'] == str(query)] to_include = list(clusterDF['Taxon']) with open(os.path.join(output, "include" + str(query) + ".txt"), "w") as i: i.write("\n".join(to_include)) # get aliases if os.path.isfile(os.path.join(species_db, "aliases.csv")): aliasDF = pd.read_csv(os.path.join(species_db, "aliases.csv")) alias_dict = get_aliases(aliasDF, list(clusterDF['Taxon']), species) else: alias_dict = {"Aliases": "NA"} return queries_names, queries_clusters, queries_prevalence, clusters, prevalences, alias_dict, to_include