diff --git a/README.md b/README.md index 6c72924..69135d7 100644 --- a/README.md +++ b/README.md @@ -75,11 +75,11 @@ Usage: plasnet split [OPTIONS] PLASMIDS DISTANCES OUTPUT_DIR Options: -d, --distance-threshold FLOAT Distance threshold -b, --bh-connectivity INTEGER Minimum number of connections a plasmid need - to be considered a blackhole plasmid + to be considered a hub plasmid -e, --bh-neighbours-edge-density FLOAT - Maximum number of edge density between - blackhole plasmid neighbours to label the - plasmid as blackhole + Maximum number of edge density between hub + plasmid neighbours to label the plasmid as + hub -p, --output-plasmid-graph Also outputs the full, unsplit, plasmid graph --plasmids-metadata PATH Plasmids metadata text file. diff --git a/plasnet/base_graph.py b/plasnet/base_graph.py index 3d30583..50d5425 100644 --- a/plasnet/base_graph.py +++ b/plasnet/base_graph.py @@ -20,19 +20,6 @@ class BaseGraph(nx.Graph): # type: ignore between the different types of graphs. """ - # def fix_node_to_subcommunity_attributes(self, node_to_subcommunity, blackhole_plasmids): - # for node, attrs in self.nodes.items(): - # if node in node_to_subcommunity: - # attrs["color"] = ColorPicker.get_color_given_index(node_to_subcommunity[node]) - # else: - # attrs["color"] = ColorPicker.get_default_color() - # - # if node in blackhole_plasmids: - # attrs["shape"] = "star" - # attrs["is_blackhole"] = True - # else: - # attrs["is_blackhole"] = False - def __init__(self, graph: Optional[nx.Graph] = None, label: str = "") -> None: super().__init__(graph) self._label = label diff --git a/plasnet/blackhole_graph.py b/plasnet/blackhole_graph.py deleted file mode 100644 index d256040..0000000 --- a/plasnet/blackhole_graph.py +++ /dev/null @@ -1,87 +0,0 @@ -import logging -from typing import Any, Optional - -import networkx as nx - -from plasnet.base_graph import BaseGraph - - -class BlackholeGraph(BaseGraph): - """ - This is a class that recognises and labels blackhole plasmids. - """ - - def __init__( - self, - graph: Optional[nx.Graph] = None, - blackhole_connectivity_threshold: int = 0, - edge_density: float = 0.0, - label: str = "", - ): - super().__init__(graph, label) - self._blackhole_connectivity_threshold = blackhole_connectivity_threshold - self._edge_density = edge_density - - def _get_node_shape(self, node: str) -> str: - if node in self._get_blackhole_plasmids(use_cached=True): - return "star" - return "circle" - - def _add_special_node_attributes(self, node: str, attrs: dict[str, Any]) -> None: - attrs["is_blackhole"] = node in self._get_blackhole_plasmids(use_cached=True) - - def _get_blackhole_plasmids(self, use_cached: bool = False) -> list[str]: - need_to_compute_the_blackhole_plasmids = not use_cached or not hasattr( - self, "_blackhole_plasmids" - ) - if need_to_compute_the_blackhole_plasmids: - blackhole_plasmids_in_graph = [] - for node in self.nodes: - if self.degree(node) >= self._blackhole_connectivity_threshold: - neighbors = list(self.neighbors(node)) - subgraph = nx.induced_subgraph(self, neighbors) - nb_of_edges_between_neighbours = subgraph.number_of_edges() - max_nb_of_edges_between_neighbours = ( - len(neighbors) * (len(neighbors) - 1) - ) // 2 - edge_rate = nb_of_edges_between_neighbours / max_nb_of_edges_between_neighbours - if edge_rate <= self._edge_density: - blackhole_plasmids_in_graph.append(node) - logging.debug(f"{node} is a blackhole plasmid") - else: - logging.debug( - f"{node} is highly connected but does not connect " - f"unrelated plasmids, not a blackhole plasmid" - ) - self._blackhole_plasmids = blackhole_plasmids_in_graph - - return self._blackhole_plasmids - - def remove_blackhole_plasmids(self) -> None: - while True: - blackhole_plasmids = self._get_blackhole_plasmids() - there_are_still_blackhole_plasmids = len(blackhole_plasmids) > 0 - if there_are_still_blackhole_plasmids: - self.remove_nodes_from(blackhole_plasmids) - else: - break - - def _get_filters_HTML(self) -> str: - nb_of_black_holes = len(self._get_blackhole_plasmids(use_cached=True)) - return ( - f'" - f'
' - ) - - def _get_custom_buttons_HTML(self) -> str: - return '
' - - @property - def description(self) -> str: - description = super().description - blackholes_detected = len(self._get_blackhole_plasmids(use_cached=True)) > 0 - if blackholes_detected: - description += " - WARNING: BLACKHOLE SPOTTED!" - return description diff --git a/plasnet/community_graph.py b/plasnet/community_graph.py index 01d00e9..f688aea 100644 --- a/plasnet/community_graph.py +++ b/plasnet/community_graph.py @@ -4,22 +4,22 @@ import networkx as nx -from plasnet.blackhole_graph import BlackholeGraph from plasnet.ColorPicker import ColorPicker +from plasnet.hub_graph import HubGraph from plasnet.subcommunities import Subcommunities from plasnet.subcommunity_graph import SubcommunityGraph from plasnet.utils import DistanceDict, DistanceTags -class CommunityGraph(BlackholeGraph): +class CommunityGraph(HubGraph): def __init__( self, graph: Optional[nx.Graph] = None, - blackhole_connectivity_threshold: int = 0, + hub_connectivity_threshold: int = 0, edge_density: float = 0.0, label: str = "", ): - super().__init__(graph, blackhole_connectivity_threshold, edge_density, label) + super().__init__(graph, hub_connectivity_threshold, edge_density, label) self._node_to_colour: dict[str, str] = {} def _get_node_color(self, node: str) -> str: @@ -87,7 +87,7 @@ def split_graph_into_subcommunities( subcommunity = SubcommunityGraph( self.subgraph(subcommunity_nodes), - self._blackhole_connectivity_threshold, + self._hub_connectivity_threshold, self._edge_density, label=f"{self.label}_subcommunity_{subcommunity_index}", colour=colour, diff --git a/plasnet/ext/templates/visualisation_template.html b/plasnet/ext/templates/visualisation_template.html index 4955b64..de2f7cc 100644 --- a/plasnet/ext/templates/visualisation_template.html +++ b/plasnet/ext/templates/visualisation_template.html @@ -217,7 +217,7 @@ 'width': 'data(size)', 'height': 'data(size)', 'shape': 'data(shape)', - 'is_blackhole': 'data(is_blackhole)' + 'is_hub': 'data(is_hub)' }, }, { @@ -235,13 +235,13 @@ - // hides blackholes - hide_blackholes = $("#hide_blackholes").is(":checked") - if (hide_blackholes) { - blackholes = cy.elements(`node[is_blackhole > 0]`) - console.log("Removing the following blackholes:") - console.log(blackholes) - cy.remove(blackholes) + // hides hubs + hide_hubs = $("#hide_hubs").is(":checked") + if (hide_hubs) { + hubs = cy.elements(`node[is_hub > 0]`) + console.log("Removing the following hubs:") + console.log(hubs) + cy.remove(hubs) } // lays out the graph @@ -279,7 +279,7 @@

But hopefully they won't be connected, so we can infer they are still different communities.

Node shapes:

● Normal plasmids

-

★ Blackhole plasmids

+

★ Hub plasmids



diff --git a/plasnet/hub_graph.py b/plasnet/hub_graph.py new file mode 100644 index 0000000..ee6ef52 --- /dev/null +++ b/plasnet/hub_graph.py @@ -0,0 +1,85 @@ +import logging +from typing import Any, Optional + +import networkx as nx + +from plasnet.base_graph import BaseGraph + + +class HubGraph(BaseGraph): + """ + This is a class that recognises and labels hub plasmids. + """ + + def __init__( + self, + graph: Optional[nx.Graph] = None, + hub_connectivity_threshold: int = 0, + edge_density: float = 0.0, + label: str = "", + ): + super().__init__(graph, label) + self._hub_connectivity_threshold = hub_connectivity_threshold + self._edge_density = edge_density + + def _get_node_shape(self, node: str) -> str: + if node in self._get_hub_plasmids(use_cached=True): + return "star" + return "circle" + + def _add_special_node_attributes(self, node: str, attrs: dict[str, Any]) -> None: + attrs["is_hub"] = node in self._get_hub_plasmids(use_cached=True) + + def _get_hub_plasmids(self, use_cached: bool = False) -> list[str]: + need_to_compute_the_hub_plasmids = not use_cached or not hasattr(self, "_hub_plasmids") + if need_to_compute_the_hub_plasmids: + hub_plasmids_in_graph = [] + for node in self.nodes: + if self.degree(node) >= self._hub_connectivity_threshold: + neighbors = list(self.neighbors(node)) + subgraph = nx.induced_subgraph(self, neighbors) + nb_of_edges_between_neighbours = subgraph.number_of_edges() + max_nb_of_edges_between_neighbours = ( + len(neighbors) * (len(neighbors) - 1) + ) // 2 + edge_rate = nb_of_edges_between_neighbours / max_nb_of_edges_between_neighbours + if edge_rate <= self._edge_density: + hub_plasmids_in_graph.append(node) + logging.debug(f"{node} is a hub plasmid") + else: + logging.debug( + f"{node} is highly connected but does not connect " + f"unrelated plasmids, not a hub plasmid" + ) + self._hub_plasmids = hub_plasmids_in_graph + + return self._hub_plasmids + + def remove_hub_plasmids(self) -> None: + while True: + hub_plasmids = self._get_hub_plasmids() + there_are_still_hub_plasmids = len(hub_plasmids) > 0 + if there_are_still_hub_plasmids: + self.remove_nodes_from(hub_plasmids) + else: + break + + def _get_filters_HTML(self) -> str: + nb_of_hubs = len(self._get_hub_plasmids(use_cached=True)) + return ( + f'" + f'
' + ) + + def _get_custom_buttons_HTML(self) -> str: + return '
' + + @property + def description(self) -> str: + description = super().description + hubs_detected = len(self._get_hub_plasmids(use_cached=True)) > 0 + if hubs_detected: + description += " - WARNING: HUB PLASMID SPOTTED!" + return description diff --git a/plasnet/output_producer.py b/plasnet/output_producer.py index d2529d9..5c0f952 100644 --- a/plasnet/output_producer.py +++ b/plasnet/output_producer.py @@ -2,8 +2,8 @@ from pathlib import Path from plasnet.base_graph import BaseGraph -from plasnet.blackhole_graph import BlackholeGraph from plasnet.communities import Communities +from plasnet.hub_graph import HubGraph from plasnet.list_of_graphs import ListOfGraphs from plasnet.Templates import Templates from plasnet.utils import get_libs_dir @@ -27,7 +27,7 @@ def produce_communities_visualisation(communities: Communities, outdir: Path) -> @staticmethod def produce_subcommunities_visualisation( - subcommunities: ListOfGraphs[BlackholeGraph], outdir: Path + subcommunities: ListOfGraphs[HubGraph], outdir: Path ) -> None: OutputProducer._write_html_for_all_subgraphs(subcommunities, outdir) OutputProducer._produce_index_file(outdir, subcommunities, "subcommunity") @@ -48,7 +48,7 @@ def _write_html_for_all_subgraphs( @staticmethod def _produce_index_file( - outdir: Path, graphs: ListOfGraphs[BlackholeGraph], objects_description: str + outdir: Path, graphs: ListOfGraphs[HubGraph], objects_description: str ) -> None: sorted_graphs = graphs.get_graphs_sorted_by_size() index_src = Templates.read_template("index_template") diff --git a/plasnet/plasnet_main.py b/plasnet/plasnet_main.py index 1fd3038..fa20209 100644 --- a/plasnet/plasnet_main.py +++ b/plasnet/plasnet_main.py @@ -72,15 +72,15 @@ def cli() -> None: "-b", type=int, default=10, - help="Minimum number of connections a plasmid need to be considered a blackhole plasmid", + help="Minimum number of connections a plasmid need to be considered a hub plasmid", ) @click.option( "--bh-neighbours-edge-density", "-e", type=float, default=0.2, - help="Maximum number of edge density between blackhole plasmid neighbours to " - "label the plasmid as blackhole", + help="Maximum number of edge density between hub plasmid neighbours to " + "label the plasmid as hub", ) @click.option( "--output-plasmid-graph", @@ -206,7 +206,7 @@ def type( logging.info("Typing communities (i.e. splitting them into subcommunities)") all_subcommunities = Subcommunities() for community in communities: - community.remove_blackhole_plasmids() + community.remove_hub_plasmids() subcommunities = community.split_graph_into_subcommunities( small_subcommunity_size_threshold ) diff --git a/plasnet/sample_graph.py b/plasnet/sample_graph.py index 365f106..d5fb808 100644 --- a/plasnet/sample_graph.py +++ b/plasnet/sample_graph.py @@ -11,13 +11,13 @@ class SampleGraph(SubcommunityGraph): def __init__( self, graph: Optional[nx.Graph] = None, - blackhole_connectivity_threshold: int = 0, + hub_connectivity_threshold: int = 0, edge_density: float = 0.0, label: str = "", colour: str = ColorPicker.get_default_color(), sample_plasmid: Optional[pd.DataFrame] = None, ): - super().__init__(graph, blackhole_connectivity_threshold, edge_density, label, colour) + super().__init__(graph, hub_connectivity_threshold, edge_density, label, colour) if sample_plasmid is not None: self._sample_to_plasmids = ( sample_plasmid.groupby("sample")["plasmid"].apply(list).to_dict() @@ -29,7 +29,7 @@ def from_subcommunity_graph( ) -> "SampleGraph": return cls( subcommunity_graph, - subcommunity_graph._blackhole_connectivity_threshold, + subcommunity_graph._hub_connectivity_threshold, subcommunity_graph._edge_density, subcommunity_graph.label, subcommunity_graph._colour, diff --git a/plasnet/subcommunity_graph.py b/plasnet/subcommunity_graph.py index 8aeb667..687d6ee 100644 --- a/plasnet/subcommunity_graph.py +++ b/plasnet/subcommunity_graph.py @@ -2,20 +2,20 @@ import networkx as nx -from plasnet.blackhole_graph import BlackholeGraph from plasnet.ColorPicker import ColorPicker +from plasnet.hub_graph import HubGraph -class SubcommunityGraph(BlackholeGraph): +class SubcommunityGraph(HubGraph): def __init__( self, graph: Optional[nx.Graph] = None, - blackhole_connectivity_threshold: int = 0, + hub_connectivity_threshold: int = 0, edge_density: float = 0.0, label: str = "", colour: str = ColorPicker.get_default_color(), ): - super().__init__(graph, blackhole_connectivity_threshold, edge_density, label) + super().__init__(graph, hub_connectivity_threshold, edge_density, label) self._colour = colour def _get_libs_relative_path(self) -> str: diff --git a/tests/data/blackhole/all_plasmids_distances.tsv b/tests/data/blackhole/all_plasmids_distances.tsv deleted file mode 100644 index 156c7a4..0000000 --- a/tests/data/blackhole/all_plasmids_distances.tsv +++ /dev/null @@ -1,1174 +0,0 @@ -plasmid_1 plasmid_2 distance -cpe004_2 cpe003_contig_3 3 -cpe004_3 cpe003_contig_4 0 -cpe007_contig_3 cpe003_contig_3 12 -cpe007_contig_3 cpe004_2 12 -cpe008_2 cpe006_contig_2 0 -cpe010_2 cpe003_contig_3 24 -cpe010_2 cpe004_2 24 -cpe010_5 cpe003_contig_4 20 -cpe010_5 cpe004_3 20 -cpe010_6 cpe009_contig_2 2 -cpe012_contig_3 cpe010_3 14 -cpe013_2 cpe003_contig_4 25 -cpe013_2 cpe004_3 25 -cpe013_2 cpe010_4 13 -cpe013_2 cpe010_5 26 -cpe013_3 cpe003_contig_4 22 -cpe013_3 cpe004_3 22 -cpe013_3 cpe010_5 28 -cpe013_3 cpe013_2 33 -cpe013_4 cpe012_contig_2 2 -cpe013_4 cpe013_2 2 -cpe014_contig_5 cpe003_contig_4 22 -cpe014_contig_5 cpe004_3 22 -cpe014_contig_5 cpe010_5 28 -cpe014_contig_5 cpe013_2 33 -cpe014_contig_5 cpe013_3 0 -cpe015_contig_2 cpe013_4 2 -cpe017_2 cpe016_contig_5 3 -cpe020_2 cpe010_3 3 -cpe020_2 cpe012_contig_3 11 -cpe020_4 cpe012_contig_2 40 -cpe022_contig_2 cpe003_contig_3 3 -cpe022_contig_2 cpe004_2 2 -cpe022_contig_2 cpe007_contig_3 12 -cpe022_contig_2 cpe010_2 26 -cpe022_contig_3 cpe003_contig_4 0 -cpe022_contig_3 cpe004_3 0 -cpe022_contig_3 cpe010_5 21 -cpe022_contig_3 cpe013_2 26 -cpe022_contig_3 cpe013_3 22 -cpe022_contig_3 cpe014_contig_5 22 -cpe023_contig_2 cpe012_contig_2 45 -cpe023_contig_2 cpe020_4 30 -cpe024_contig_2 cpe020_3 17 -cpe024_contig_3 cpe012_contig_2 19 -cpe024_contig_3 cpe020_4 44 -cpe024_contig_3 cpe023_contig_2 40 -cpe025_contig_2 cpe009_contig_3 3 -cpe025_contig_6 cpe015_contig_4 16 -cpe027_2 cpe003_contig_4 32 -cpe027_2 cpe004_3 32 -cpe027_2 cpe010_5 27 -cpe027_2 cpe013_2 32 -cpe027_2 cpe013_3 21 -cpe027_2 cpe014_contig_5 21 -cpe027_2 cpe022_contig_3 30 -cpe027_3 cpe012_contig_2 28 -cpe027_3 cpe020_4 49 -cpe027_3 cpe023_contig_2 46 -cpe027_3 cpe024_contig_3 37 -cpe028_contig_4 cpe009_contig_3 0 -cpe028_contig_4 cpe025_contig_2 3 -cpe029_contig_3 cpe028_contig_2 0 -cpe029_contig_4 cpe003_contig_4 28 -cpe029_contig_4 cpe004_3 28 -cpe029_contig_4 cpe010_4 12 -cpe029_contig_4 cpe010_5 35 -cpe029_contig_4 cpe013_2 25 -cpe029_contig_4 cpe013_3 34 -cpe029_contig_4 cpe014_contig_5 34 -cpe029_contig_4 cpe022_contig_3 29 -cpe029_contig_4 cpe027_2 36 -cpe029_contig_5 cpe009_contig_3 0 -cpe029_contig_5 cpe025_contig_2 3 -cpe029_contig_5 cpe028_contig_4 0 -cpe034_2 cpe003_contig_3 5 -cpe034_2 cpe004_2 3 -cpe034_2 cpe007_contig_3 12 -cpe034_2 cpe010_2 24 -cpe034_2 cpe022_contig_2 4 -cpe034_3 cpe003_contig_4 29 -cpe034_3 cpe004_3 29 -cpe034_3 cpe010_4 9 -cpe034_3 cpe010_5 22 -cpe034_3 cpe013_2 26 -cpe034_3 cpe022_contig_3 29 -cpe034_3 cpe027_2 33 -cpe034_3 cpe029_contig_4 28 -cpe034_4 cpe003_contig_4 1 -cpe034_4 cpe004_3 1 -cpe034_4 cpe010_5 21 -cpe034_4 cpe013_2 24 -cpe034_4 cpe013_3 21 -cpe034_4 cpe014_contig_5 21 -cpe034_4 cpe022_contig_3 1 -cpe034_4 cpe027_2 31 -cpe034_4 cpe029_contig_4 29 -cpe034_4 cpe034_3 27 -cpe035_contig_1 cpe003_contig_3 5 -cpe035_contig_1 cpe004_2 3 -cpe035_contig_1 cpe007_contig_3 12 -cpe035_contig_1 cpe010_2 26 -cpe035_contig_1 cpe022_contig_2 4 -cpe035_contig_1 cpe034_2 4 -cpe035_contig_3 cpe003_contig_4 17 -cpe035_contig_3 cpe004_3 17 -cpe035_contig_3 cpe010_4 9 -cpe035_contig_3 cpe010_5 24 -cpe035_contig_3 cpe013_2 30 -cpe035_contig_3 cpe013_3 31 -cpe035_contig_3 cpe014_contig_5 31 -cpe035_contig_3 cpe022_contig_3 17 -cpe035_contig_3 cpe027_2 36 -cpe035_contig_3 cpe029_contig_4 30 -cpe035_contig_3 cpe034_3 12 -cpe035_contig_3 cpe034_4 15 -cpe035_contig_9 cpe003_contig_4 1 -cpe035_contig_9 cpe004_3 1 -cpe035_contig_9 cpe010_5 22 -cpe035_contig_9 cpe013_2 24 -cpe035_contig_9 cpe013_3 21 -cpe035_contig_9 cpe014_contig_5 21 -cpe035_contig_9 cpe022_contig_3 1 -cpe035_contig_9 cpe027_2 29 -cpe035_contig_9 cpe029_contig_4 27 -cpe035_contig_9 cpe034_3 27 -cpe035_contig_9 cpe034_4 0 -cpe035_contig_9 cpe035_contig_3 15 -cpe037_contig_6 cpe016_contig_2 28 -cpe040_contig_3 cpe012_contig_2 28 -cpe040_contig_3 cpe020_4 35 -cpe040_contig_3 cpe023_contig_2 35 -cpe040_contig_3 cpe024_contig_3 27 -cpe040_contig_3 cpe027_3 41 -cpe040_contig_4 cpe009_contig_3 7 -cpe040_contig_4 cpe025_contig_2 9 -cpe040_contig_4 cpe028_contig_4 7 -cpe040_contig_4 cpe029_contig_5 7 -cpe040_contig_5 cpe024_contig_6 12 -cpe041_contig_1 cpe012_contig_2 15 -cpe041_contig_1 cpe023_contig_2 30 -cpe041_contig_1 cpe024_contig_3 18 -cpe041_contig_1 cpe027_3 17 -cpe041_contig_1 cpe040_contig_3 25 -cpe041_contig_3 cpe040_contig_6 26 -cpe041_contig_4 cpe027_4 2 -cpe042_2 cpe010_3 22 -cpe042_2 cpe012_contig_3 16 -cpe042_2 cpe020_2 19 -cpe043_3 cpe009_contig_3 9 -cpe043_3 cpe025_contig_2 12 -cpe043_3 cpe028_contig_4 9 -cpe043_3 cpe029_contig_5 9 -cpe043_3 cpe040_contig_4 9 -cpe044_contig_4 cpe011_2 2 -cpe045_2 cpe044_contig_2 12 -cpe045_3 cpe011_2 0 -cpe045_3 cpe044_contig_4 2 -cpe047_3 cpe003_contig_4 25 -cpe047_3 cpe004_3 25 -cpe047_3 cpe013_3 24 -cpe047_3 cpe014_contig_5 24 -cpe047_3 cpe022_contig_3 23 -cpe047_3 cpe027_2 10 -cpe047_3 cpe034_4 24 -cpe047_3 cpe035_contig_9 22 -cpe047_4 cpe012_contig_2 16 -cpe047_4 cpe023_contig_2 16 -cpe047_4 cpe027_3 13 -cpe047_4 cpe040_contig_3 10 -cpe047_4 cpe041_contig_1 18 -cpe047_6 cpe027_4 0 -cpe047_6 cpe041_contig_4 2 -cpe049_contig_2 cpe029_contig_4 32 -cpe049_contig_3 cpe003_contig_4 34 -cpe049_contig_3 cpe004_3 34 -cpe049_contig_3 cpe010_5 28 -cpe049_contig_3 cpe013_2 35 -cpe049_contig_3 cpe013_3 33 -cpe049_contig_3 cpe014_contig_5 33 -cpe049_contig_3 cpe022_contig_3 32 -cpe049_contig_3 cpe027_2 34 -cpe049_contig_3 cpe029_contig_4 32 -cpe049_contig_3 cpe034_3 34 -cpe049_contig_3 cpe034_4 35 -cpe049_contig_3 cpe035_contig_3 35 -cpe049_contig_3 cpe035_contig_9 33 -cpe049_contig_3 cpe047_3 26 -cpe049_contig_4 cpe012_contig_2 32 -cpe049_contig_4 cpe020_4 33 -cpe049_contig_4 cpe023_contig_2 40 -cpe049_contig_4 cpe024_contig_3 27 -cpe049_contig_4 cpe027_3 14 -cpe049_contig_4 cpe040_contig_3 29 -cpe051_contig_2 cpe012_contig_2 16 -cpe051_contig_2 cpe023_contig_2 29 -cpe051_contig_2 cpe024_contig_3 18 -cpe051_contig_2 cpe027_3 18 -cpe051_contig_2 cpe040_contig_3 25 -cpe051_contig_2 cpe041_contig_1 2 -cpe051_contig_2 cpe047_4 19 -cpe051_contig_3 cpe027_4 2 -cpe051_contig_3 cpe041_contig_4 0 -cpe051_contig_3 cpe047_6 2 -cpe052_2 cpe010_5 17 -cpe052_2 cpe013_3 15 -cpe052_2 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and /dev/null differ diff --git a/tests/data/blackhole/truth_typing.tsv b/tests/data/blackhole/truth_typing.tsv deleted file mode 100644 index beb1036..0000000 --- a/tests/data/blackhole/truth_typing.tsv +++ /dev/null @@ -1,193 +0,0 @@ -plasmid type -cpe007_contig_3 community_0_subcommunity_0 -cpe010_2 community_0_subcommunity_1 -cpe010_5 community_0_subcommunity_2 -cpe010_4 community_0_subcommunity_3 -cpe020_4 community_0_subcommunity_4 -cpe020_3 community_0_subcommunity_5 -cpe024_contig_3 community_0_subcommunity_6 -cpe027_2 community_0_subcommunity_7 -cpe027_3 community_0_subcommunity_8 -cpe029_contig_4 community_0_subcommunity_9 -cpe034_3 community_0_subcommunity_10 -cpe035_contig_3 community_0_subcommunity_11 -cpe040_contig_3 community_0_subcommunity_12 -cpe047_3 community_0_subcommunity_13 -cpe049_contig_2 community_0_subcommunity_14 -cpe049_contig_3 community_0_subcommunity_15 -cpe049_contig_4 community_0_subcommunity_16 -cpe060_2 community_0_subcommunity_17 -cpe067_2 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--git a/tests/data/blackhole/.gitignore b/tests/data/hub/.gitignore similarity index 100% rename from tests/data/blackhole/.gitignore rename to tests/data/hub/.gitignore diff --git a/tests/data/hub/all_pairs_jaccard_distance.tsv b/tests/data/hub/all_pairs_jaccard_distance.tsv new file mode 100644 index 0000000..eb188b5 --- /dev/null +++ b/tests/data/hub/all_pairs_jaccard_distance.tsv @@ -0,0 +1,2851 @@ +plasmid_1 plasmid_2 distance +pCAV1043-1919 pCAV1043-10 0.7759249609171444 +pCAV1043-51 pCAV1043-10 0.7937133519177161 +pCAV1043-51 pCAV1043-1919 1.0 +pCAV1043-58 pCAV1043-10 1.0 +pCAV1043-58 pCAV1043-1919 1.0 +pCAV1043-58 pCAV1043-51 0.9840026499873347 +pCAV1043-97 pCAV1043-10 0.4410266269345381 +pCAV1043-97 pCAV1043-1919 1.0 +pCAV1043-97 pCAV1043-51 0.827614426842813 +pCAV1043-97 pCAV1043-58 0.97985520392969 +pCAV1099-111 pCAV1043-10 1.0 +pCAV1099-111 pCAV1043-1919 1.0 +pCAV1099-111 pCAV1043-51 1.0 +pCAV1099-111 pCAV1043-58 1.0 +pCAV1099-111 pCAV1043-97 1.0 +pCAV1099-114 pCAV1043-10 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0.765356211029054 diff --git a/tests/data/blackhole_2/all_plasmids_distances.tsv b/tests/data/hub/all_plasmids_distances.tsv similarity index 100% rename from tests/data/blackhole_2/all_plasmids_distances.tsv rename to tests/data/hub/all_plasmids_distances.tsv diff --git a/tests/data/hub/plasmids.tsv b/tests/data/hub/plasmids.tsv new file mode 100644 index 0000000..1a4b209 --- /dev/null +++ b/tests/data/hub/plasmids.tsv @@ -0,0 +1,77 @@ +plasmid +pCAV1043-10 +pCAV1043-1919 +pCAV1043-51 +pCAV1043-58 +pCAV1043-97 +pCAV1099-111 +pCAV1099-114 +pCAV1099-5410 +pCAV1099-69 +pCAV1151-215 +pCAV1151-296 +pCAV1151-83 +pCAV1176-3223 +pCAV1176-34 +pCAV1311-3223 +pCAV1311-34 +pCAV1321-135 +pCAV1321-1916 +pCAV1321-3223 +pCAV1321-3820 +pCAV1321-4310 +pCAV1321-4938 +pCAV1321-71 +pCAV1335-115 +pCAV1335-118 +pCAV1335-5410 +pCAV1335-92 +pCAV1344-250 +pCAV1344-3741 +pCAV1344-40 +pCAV1344-78 +pCAV1374-14 +pCAV1374-150 +pCAV1374-16 +pCAV1374-1919 +pCAV1374-228 +pCAV1374-34 +pCAV1374-49 +pCAV1374-54 +pCAV1374-6538 +pCAV1374-84 +pCAV1392-131 +pCAV1392-50 +pCAV1411-34 +pCAV1492-199 +pCAV1492-3223 +pCAV1492-6393 +pCAV1492-73 +pCAV1596-2927 +pCAV1596-41 +pCAV1668-85 +pCAV1669-34 +pCAV1741-101 +pCAV1741-110 +pCAV1741-16 +pCAV1741-1916 +pCAV1741-3223 +pKPC_CAV1043 +pKPC_CAV1099 +pKPC_CAV1151 +pKPC_CAV1176 +pKPC_CAV1311 +pKPC_CAV1320 +pKPC_CAV1321-244 +pKPC_CAV1321-45 +pKPC_CAV1335 +pKPC_CAV1344 +pKPC_CAV1374 +pKPC_CAV1392 +pKPC_CAV1411 +pKPC_CAV1492 +pKPC_CAV1596-78 +pKPC_CAV1596-97 +pKPC_CAV1668 +pKPC_CAV1669 +pKPC_CAV1741 diff --git a/tests/data/blackhole_2/truth_typing.tsv b/tests/data/hub/truth_typing.tsv similarity index 100% rename from tests/data/blackhole_2/truth_typing.tsv rename to tests/data/hub/truth_typing.tsv diff --git a/tests/data/subcommunities.pkl b/tests/data/subcommunities.pkl index 42bd417..ed6630f 100644 Binary files a/tests/data/subcommunities.pkl and b/tests/data/subcommunities.pkl differ diff --git a/tests/test_integration_tests.py b/tests/test_integration_tests.py index a2921a0..cf9505e 100644 --- a/tests/test_integration_tests.py +++ b/tests/test_integration_tests.py @@ -74,45 +74,42 @@ def test_add_sample_hits_command(self) -> None: self.assertEqual(result.exit_code, 0) -class TestRemoveBlackholePlasmids(TestCase): - def test_remove_blackhole_plasmids(self) -> None: +class TestRemoveHubPlasmidsIteratively(TestCase): + def test_remove_hub_plasmids_iteratively(self) -> None: runner = CliRunner() result = runner.invoke( cli, [ - "type", - "tests/data/blackhole/communities.pkl", - "tests/data/blackhole/all_plasmids_distances.tsv", - "tests/data/blackhole/out", + "split", + "tests/data/hub/plasmids.tsv", + "tests/data/hub/all_pairs_jaccard_distance.tsv", + "tests/data/hub/out/split_out", + "--distance-threshold", + "0.6", + "--bh-connectivity", + "10", + "--bh-neighbours-edge-density", + "0.2", + "--output-plasmid-graph", ], ) self.assertEqual(result.exit_code, 0) - self.assertTrue( - check_if_files_are_equal( - Path("tests/data/blackhole/out/objects/typing.tsv"), - Path("tests/data/blackhole/truth_typing.tsv"), - sort=True, - ) - ) - -class TestRemoveBlackholePlasmidsIteratively(TestCase): - def test_remove_blackhole_plasmids_iteratively(self) -> None: - runner = CliRunner() result = runner.invoke( cli, [ "type", - "tests/data/blackhole_2/communities.pkl", - "tests/data/blackhole_2/all_plasmids_distances.tsv", - "tests/data/blackhole_2/out", + "tests/data/hub/out/split_out/objects/communities.pkl", + "tests/data/hub/all_plasmids_distances.tsv", + "tests/data/hub/out/type_out", ], ) self.assertEqual(result.exit_code, 0) + self.assertTrue( check_if_files_are_equal( - Path("tests/data/blackhole_2/out/objects/typing.tsv"), - Path("tests/data/blackhole_2/truth_typing.tsv"), + Path("tests/data/hub/out/type_out/objects/typing.tsv"), + Path("tests/data/hub/truth_typing.tsv"), sort=True, ) )