Command Line Manual

Pyntacle version 1.0


Table of contents

General Options


  • -h/--help: Shows this help message and exit
  • -v: Verbosity level of the internal Pyntacle logger. -vvv is the highest level (for debugging purposes).
  • -V/ --version: Shows program version number and quits.

Pyntacle Commands - Description and Usage


keyplayer
Description

Computes key player metrics for a specific set of nodes (kp-info) or find a set of node of size k that owns the optimal or the best score (kp-finder).

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Usage Examples

pyntacle keyplayer kp-finder -i input.adjm -f adjm -m 2 -k 3 --seed 100 -M 2 -t pos --save-binary --plot-format svg --plot-dim 1920,1080

pyntacle keyplayer kp-finder -i input.egl -f egl --input-separator ";" -k 2 -I brute-force -t dF -r xlsx

pyntacle keyplayer kp-info -i input.sif --nodes A,B,C --t neg --no-header --no-plot


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Common arguments of "keyplayer kp-info" and "keyplayer kp-finder"
  • -i , --input-file (required): Path to the network input file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): Input network file format. Different formats can be specified using different keywords; If not specified, the input format will be guessed. See the following table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
  • --input-separator: The field separator for the input file. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -t/--type: The key player metric (or metrics) of interest. Choices are:
    • all: all metrics
    • pos: reachabiliy metrics: dR and m-reach
    • neg: fragmentation metrics: F and dF
    • dR
    • m-reach
    • F
    • dF
    Default is all.
  • -m/--m-reach (required for m-reach): The maximum distance that will be used to compute the m-reach metric. Must be provided if m-reach is computed.
  • -L/--largest-component: Considers only the largest component of the input graph and excludes the smaller ones.It will raise an error if the network has two largest components of the same size.
  • -M/--max-distance: The number of steps after which two nodes will be considered as disconnected. By default, no maximum distance is set.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -r/--report-format: The format of the report produced by Pyntacle. Choices are:
    • txt and tsv: tab-separated file
    • csv: comma-separated value file
    • xlsx: Excel file
    Defaults to txt.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Bypassed if --no-plot is specified or the graph exceeds the maximum number of nodes. You can find a detailed description of each layout and all the alternate keywords that can alternatively be passed instead of full names in the table below:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
  • --no-plot: Skips the graphical representation of the plot.
  • --save-binary: Saves a binary file (ending in .graph) that contains the network and all the operations performed on it in an igraph.Graph object.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: Shows the help message for the pyntacle keyplayer command and exits.

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Subcommands

kp-finder
Description

Find the best kp set of size k using key player metrics and either a greedy or a bruteforce algorithm.

Specific Arguments
  • -k/--k-size (required): An integer specifying the size of the node set size.
  • -I/--implementation: The strategy used for the search of the node set. Choices are:
    • greedy: a greedy optimization algorithm aimed at finding an optimal solution)
    • brute-force: a brute-force search that find the best solution (or solutions).
    greedy is the default strategy.
  • -S/--seed (greedy optimization only): Sets a user-defined seed to replicate the greedy optimization search.
  • -O/--nprocs (brute-force search only): Specifies the number of processes that will be forked during the execution of the brute-force search algorithm. Default to 1.
kp-info
Description

Computes specified key player metrics for a selected subset of nodes.

Specific Arguments
  • -n/--nodes (required): Comma-separated list of strings, corresponding to the node names in the input graph, or column index of the input network file if the no-header flag is specified.

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groupcentrality
Description

Computes group centrality metrics, a variation of classical node centrality indices. These metrics can be computed for a specific set of nodes (gr-info) or they can be used to find a set of node of size k that own the optimal or the best score (gr-finder).

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Usage Examples

pyntacle groupcentrality gr-finder -i input.sif -k 3 --seed 100 --group-distance mean -t closeness --save-binary --plot-dim 1920,1080

pyntacle groupcentrality gr-finder -i input.egl -f egl --input-separator ";" -k 2 -I brute-force -t betweenness -r xlsx

pyntacle groupcentrality gr-info -i input.bin --nodes A,B --t degree --no-header --no-plot


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Common arguments of "groupcentrality gc-info" and "groupcentrality gc-finder"
  • -i , --input-file (required): Path to the network input file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): Input network file format. Different formats can be specified using different keywords; If not specified, the input format will be guessed. See the following table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
    See the Pyntacle file formats guide for more information and other available abbreviations. If not specified, the input format will be guessed.
  • --input-separator: The field separator for the input file. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -t/--type: The group centrality metric (or metrics) of interest. Choices are:
    • all (all metrics)
    • degree (group degree only)
    • closeness (group closeness)
    • betweenness (group betweenness)
    Default is all.
  • -D/--group-distance (required for group closeness): The criterion to use to compute the distance between the node set and the rest of the graph. Choices are:
    • mean (averages the distances among the node set and the rest of the graph)
    • min (takes the minimum distance among the node set and the rest of the graph)
    • max (takes the maximum distance among the node set and the rest of the graph)
    Defaults to min.
  • -L/--largest-component: Considers only the largest component of the input graph and excludes the smaller ones. It will raise an error if the network has two largest components of the same size.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, we will create one at the specified path. Default is the current working directory.
  • -r/--report-format: The format of the report produced by Pyntacle. Choices are:
    • txt and tsv (tab-separated file)
    • csv (comma-separated value file)
    • xlsx (Excel file)
    Defaults to txt.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes). Overridden by --no-plot.
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Choices are listed in the following table:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
    Default is fruchterman_reingold. Bypassed if the --no-plot flag if specified or if the graph is too big to be represented (larger than 1000 nodes).
  • --no-plot: Skips the graphical representation of the plot.
  • --save-binary: Saves a binary file (ending in .graph)that contains the network and all the operations performed on it in an igraph.Graph object.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: show help message for the pyntacle groupcentrality command and exits.

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Subcommands

gr-finder
Description

Finds the optimal or the best set of size k for a group centrality index (or indices) by means of either a greedy optimization or a brute-force algorithm.

Specific Arguments
  • -k/--k-size (required): An integer specifying the size of the node set size.
  • -I/--implementation: The strategy used for the search of the node set. Choices are:
    • greedy: a greedy optimization algorithm aimed at finding an optimal solution
    • brute-force: a brute-force search that find the best solution (or solutions).
    greedy is the default strategy.
  • -S/--seed (greedy optimization only): Sets a user-defined seed to replicate the greedy optimization search.
  • -O/--nprocs (brute-force search only): Specifies the number of processes that will be forked during the execution of the brute-force search algorithm. Default to 1.
gr-info
Description

Computes all or a selected group-centrality metric for a selected subset of nodes.

Specific Arguments
  • -n/--nodes (required): Comma-separated list of strings, corresponding to the node names in the input graph, or column index of the input network file if the no-header flag is specified.

metrics
Description

Compute various types of metrics for a set of nodes of a network or for the whole graph.


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Usage Examples

pyntacle metrics local --nodes A,B,C -i input.adjm -f adjm --input-separator "\t" --largest-component --plot-dim 400,600

pyntacle metrics global input.dot -d ./ --report-format csv --no-plot --save-binary


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Common arguments of "local" and "global"
  • -i , --input-file (required): Path to the network input file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): Input network file format. Different formats can be specified using different keywords; If not specified, the input format will be guessed. See the following table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
  • --input-separator: The field separator for the input file. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -L/--largest-component: Considers only the largest component of the input graph and excludes the smaller ones.It will raise an error if the network has two largest components of the same size.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -r/--report-format: The format of the report produced by Pyntacle. Choices are:
    • txt and tsv: tab-separated file
    • csv: comma-separated value file
    • xlsx: Excel file
    Defaults to txt.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Bypassed if --no-plot is specified or the graph exceeds the maximum number of nodes. You can find a detailed description of each layout and all the alternate keywords that can alternatively be passed instead of full names in the table below:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
  • --no-plot: Skips the graphical representation of the plot.
  • --save-binary: Saves a binary file (ending in .graph) that contains the network and all the operations performed on it in an igraph.Graph object.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: Shows the help message for the pyntacle keyplayer command and exits.

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Subcommands

local
Description

Computes local centrality measures for a single node, a group of nodes or all nodes in the graph.

Specific Arguments
  • -n/--nodes (required): Comma-separated list of strings, corresponding to the node names in the input graph, or column index of the input network file if the 'no-header' flag is specified. If not specified, local centrality indiceswill be computed for all nodes in the input graph.
  • --damping-factor: A float specifying the damping factor that will be used to compute the PageRank index. Default is 0.85.
  • -w/--weights: Path to an edge attribute file storing weights that will be used to compute the PageRank index. Must be either a Standard Edge Attribute Format or a Ctyotscape Edge Attribute format. See File Format Specifications for more details on edge attribute files. NOTE: a column named 'weights' must be present in the edge attribute file.
  • --weights-format (required for --weights): The format of the input edge attribute file. Choices are:
    • standard: a standard edge attributes file
    • cytoscape: the Cytoscape legacy attribute file.
    See File Format Specifications for more details on edge attribute files. Default is standard.
global
Description

Computes global centrality measures for the whole graph. Can also be used to remove nodes from the graph and computing these global centrality measures before and after the node removal.

Specific Arguments
  • -n/--no-nodes: Comma-separated list corresponding to vertices names or a list of indices matching the column index in the node adjacency matrix if no-header is specified. These nodes will be removed from the input graph, and global metrics will be computed before and after the node removal.Remove a set of nodes and compute global metrics without these nodes.

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communities
Description

Detects communities of tightly connected nodes within a graph by means of different modular decomposition algorithms. Produces several network files, each one containing an induced subgraph of every community found. The resulting communities can be filtered by thenumber of nodes or components


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Usage Examples

pyntacle communities fastgreedy -i input.egl -f edgelist -u sif -o results --min-nodes 10 --no-output-header --clusters 10

pyntacle communities community-walktrap -i input.adjm --steps 8 --weights input.wgh -d ./pyntacle-results --no-plot

pyntacle communities leading-eigenvector -i input.graph -o results --no-output-header -u adjm --max-nodes 200

pyntacle communities infomap -i input.sif --no-header --max-components 3 --no-plot --save-binary --output-separator “,”


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Common arguments
  • -i , --input-file (required): Path to the network input file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): Input network file format. Different formats can be specified using different keywords; If not specified, the input format will be guessed. See the following table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
  • --input-separator: The field separator for the input file. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -L/--largest-component: Considers only the largest component of the input graph and excludes the smaller ones.It will raise an error if the network has two largest components of the same size.
  • -m/--min-nodes: Filters the resulting communities and keeps only those with a number of vertices equal or greater than this treshold.
  • -M/--max-nodes: Filters the resulting communities and keeps only those with a number of vertices equal or lesser than this threshold.
  • -c/--min-components: Filters the resulting communities and keeps only those with a number of components equal or greater than this threshold.
  • -C/--max-components: Filters the resulting communities and keeps only those with a number of components equal or greater than this threshold.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -o/--output-file: Basename of the output network files. If not specified, a standard name will be generated.
  • -u/--output-format: Desired output format for the output network files storing communities. The same abbreviations used in the '--format' are applied. See File Format Specifications for more details. Default is adjmat (Adjacency Matrix).
  • --output-separator: The field separator of the output network file. Default is ' '. NOTE: the separator must be wrapped in quotes.
  • --no-output-header: Skips the creation of a header for the resulting network files if the output format is an adjacency matrix, an edge list or a SIF file. See File Format Specifications for more details. If not specified, the output network files will contain a header by default.
  • -r/--report-format: The format of the report produced by Pyntacle. Choices are:
    • txt and tsv (tab-separated file)
    • csv (comma-separated value file)
    • xlsx (Excel file)
    Defaults to txt.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Bypassed if --no-plot is specified or the graph exceeds the maximum number of nodes. You can find a detailed description of each layout and all the alternate keywords that can alternatively be passed instead of full names in the table below:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
  • --no-plot: Skips the graphical representation of the plot.
  • --save-binary: Saves a binary file (ending in .graph) that contains the network and all the operations performed on it in an igraph.Graph object.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: Shows the help message for the pyntacle keyplayer command and exits.

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Subcommands

fastgreedy
Description

Modular decomposition by means of the fastgreedy algorithm

Specific Arguments
  • --clusters: Specifies the number of clusters around which the modular decomposition algorithm will optimize its module search.
    • -w/--weights: Path to an edge attribute file storing weights that will be used to compute the PageRank index. Must be either a Standard Edge Attribute Format or a Ctyotscape Edge Attribute format. See File Format Specifications for more details on edge attribute files. NOTE: a column named 'weights' must be present in the edge attribute file.
  • --weights-format (required for --weights): The format of the input edge attribute file. Choices are:
    • standard: a standard edge attributes file
    • cytoscape: the Cytoscape legacy attribute file.
    See File Format Specifications for more details on edge attribute files. Default is standard.
infomap
Description

Modular decomposition by means of the naive implementation of the infomap algorithm.

Specific Arguments
  • NO SPECIFIC ARGUMENTS.
leading-eigenvector
Description

Modular decomposition computing the leading eigenvectors for each community.

Specific Arguments
  • NO SPECIFIC ARGUMENTS.
community-walktrap
Description

Modular decomposition by means of random walks within the graph.

Specific Arguments
  • --steps: Specifies the maximum number of steps for the random walker. High number of steps leads to lesser cohese communities. Default is 3.
  • --clusters: Specifies the number of clusters around which the modular decomposition algorithm will optimize its module search.
  • -w/--weights: Path to an edge attribute file storing weights that will be used to compute the PageRank index. Must be either a Standard Edge Attribute Format or a Ctyotscape Edge Attribute format. See File Format Specifications for more details on edge attribute files. NOTE: a column named 'weights' must be present in the edge attribute file.
  • --weights-format (required for --weights): The format of the input edge attribute file. Choices are:
    • standard: a standard edge attributes file
    • cytoscape: the Cytoscape legacy attribute file.
    See File Format Specifications for more details on edge attribute files. Default is standard.

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set
Description

Performs set operations (union, intersection, difference) between two networks using logical graph operations.


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Usage Examples

pyntacle set union -1 input_1.adjm -2 input_2.adjm -f adjm -u sif --largest-component -d . --output-separator ","

pyntacle set intersection -1 input_1.edgl -2 input_2.edgl-f egl -u adjm --report-format xlsx --plot-dim 1600,1600 -d results/

pyntacle set difference -1 input_1.sif -2 input_2.sif -f egl -u dot -o final --report-format xlsx --no-plot


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Common arguments
  • -1 , --input-file-1 (required): Path to the first input network file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -2 , --input-file-2 (required): Path to the second input network file. It can be an adjacency matrix, an edge list, a Simple Interaction (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): specifies the format of the input file passed using the -1/--input-file-1 and the -2/--input-file-2 command. Different file formats can be specified using different keywords. See the follwing table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
    NOTE: The two network files MUST have the same format. If not, use pyntacle convert to convert them to a common accepted network file format.
  • --input-separator: The field separator for the input files. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -L/--largest-component: Considers only the largest component of the input graph and excludes the smaller ones.It will raise an error if the network has two largest components of the same size.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -o/--output-file: Basename of the output network files. If not specified, a standard name will be generated.
  • -u/--output-format: Desired output format for the output network files storing communities. The same abbreviations used in the '--format' are applied. See File Format Specifications for more details. Default is adjmat (Adjacency Matrix).
  • --output-separator: The field separator of the output network file. Default is ' '. NOTE: the separator must be wrapped in quotes.
  • --no-output-header: Skips the creation of a header for the resulting network files if the output format is an adjacency matrix, an edge list or a SIF file. See File Format Specifications for more details. If not specified, the output network files will contain a header by default.
  • -r/--report-format: The format of the report produced by Pyntacle. Choices are:
    • txt and tsv (tab-separated file)
    • csv (comma-separated value file)
    • xlsx (Excel file)
    Defaults to txt.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Bypassed if --no-plot is specified or the graph exceeds the maximum number of nodes. You can find a detailed description of each layout and all the alternate keywords that can alternatively be passed instead of full names in the table below:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
  • --no-plot: Skips the graphical representation of the plot.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: Shows the help message for the pyntacle keyplayer command and exits.

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Subcommands

intersection
Description

Graph intersection. Returns only the common nodes and their connecting edges among the two graphs of interest.

Specific Arguments
  • NO SPECIFIC ARGUMENTS.
union
Description

Graph union. Returns a resulting merged graph of the original two networks, marking the common nodes among them along with their common connecting edges.

Specific Arguments
  • NO SPECIFIC ARGUMENTS.
difference
Description

Performs the difference between the two input graphs. Returns the nodes and edges belonging only to the first input graph. NOTE: the difference among graphs is not reciprocal.

Specific Arguments
  • NO SPECIFIC ARGUMENTS.

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convert
Description

Converts a network file from one format to another.


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Usage Examples

pyntacle convert -i input.sif -u edgl --no-output-header

pyntacle convert -i input.dot -u bin -f dot -o final

pyntacle convert -i input.edgl -f egl -u adjm -d /home/results/


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Arguments
  • -i , --input-file (required): Path to the network input file. It can be an adjacency matrix, an edge list, a Simple Interaction Format (SIF) file, a DOT file or a binary storing an igraph.Graph object. See File Format Specifications for more details.
  • -f/--format (recommended): Input network file format. Different formats can be specified using different keywords; If not specified, the input format will be guessed. See the following table for detailed information of all available options:
    File Type Keywords
    adjacency matrix adjacencymatrix, adjacency_matrix, adjmat, adjm
    edge list edgelist, edge_list, edgl, egl
    Simple Interaction Format (SIF) sif
    DOT File dot
    binary binary, bin, graph
  • --input-separator: The field separator for the input file. If not provided, Pyntacle tries to guess it automatically.
  • -N/--no-header: A flag that must be used if the input network file (adjacency matrix, edge list, SIF file) does not contain a header. By default, we assume a header is present.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -o/--output-file: Basename of the output network files. If not specified, a standard name will be generated.
  • -u/--output-format: Desired output format for the output network files storing communities. The same abbreviations used in the '--format' are applied. See File Format Specifications for more details. Default is adjmat (Adjacency Matrix).
  • --output-separator: The field separator of the output network file. Default is ' '. NOTE: the separator must be wrapped in quotes.
  • --no-output-header: Skips the creation of a header for the resulting network files if the output format is an adjacency matrix, an edge list or a SIF file. See File Format Specifications for more details. If not specified, the output network files will contain a header by default.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: show help message for the pyntacle convert command and exits.

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generate
Description

Generates in silico networks based on a series of predetermined topologies.


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Usage Examples

pyntacle generate random -n 10 -p 0.3 -u sif -o random_1 -R 3

pyntacle generate small-world -p 0.8 -n 2 -u adjm -d /home/results/

pyntacle generate scale-free -n 200 -m 2 -o scalefree_10 --no-plot

pyntacle generate tree -n 50 -c 2 -u dot --plot-format svg


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Common arguments
  • -R/--repeat: Repeats the graph generation for 'n' times. NOTE: --repeat overrides --seed.
  • -S/--seed: Sets a seed when creating a network, to replicate the network construction. NOTE: overridden by --repeat.
  • -d/--directory: The directory that will store Pyntacle results. If the directory does not exist, it will be created at the desired location. Default is the current working directory.
  • -o/--output-file: Basename of the output network files. If not specified, a standard name will be generated.
  • -u/--output-format: Desired output format for the output network files storing communities. The same abbreviations used in the '--format' are applied. See File Format Specifications for more details. Default is adjmat (Adjacency Matrix).
  • --output-separator: The field separator of the output network file. Default is ' '. NOTE: the separator must be wrapped in quotes.
  • --no-output-header: Skips the creation of a header for the resulting network files if the output format is an adjacency matrix, an edge list or a SIF file. See File Format Specifications for more details. If not specified, the output network files will contain a header by default.
  • -P/--plot-format: The format for the network representation produced by Pyntacle. Choices are:
    • pdf
    • png
    • svg
    Defaults to pdf. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-dim: The dimensions (as comma-separated values) of the graphical representation of the results. Default is 800,800 for graph with less than 150 nodes and 1600,1600 otherwise. Overridden by the --no-plot flag or if the graph is too big to be represented (larger than 1000 nodes).
  • --plot-layout: Specifies one of the predefined layout for the graphical representation of the network. Bypassed if --no-plot is specified or the graph exceeds the maximum number of nodes. You can find a detailed description of each layout and all the alternate keywords that can alternatively be passed instead of full names in the table below:
    Layout Keywords Useful with
    Fruchterman-Reingold fruchterman_reingold, fr Modular, loosely sparse loosely sparse networks (e.g. Scale-free)
    Kamada-Kawai kamada-kawai, kk Networks with very distinct communities (as an alternative to fruchterman-reingold)
    Large-Graph large_graph, lgl Large and dense graphs
    Random random Random structures
    Reingold-Tilford reingold_tilford, rt Networks with distinct hierarchies (e.g. Trees)
  • --no-plot: Skips the graphical representation of the plot.
  • --suppress-cursor: Suppresses the animated cursor during Pyntacle execution.
  • -h/--help: show help message for the pyntacle generate command and exits.

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Subcommands

random
Description

Random network created using the Erdos–Renyi model.

Specific Arguments
  • -n/--nodes: Number of vertices of the resulting random graph. If not specified, it will be a number between 100 and 500 (chosen randomly)
  • -p/--probability: The wiring probability to connect each node pair. Must be a float between 0 and 1. Default is 0.5. Overrides -e/--edges.
  • -e/--edges: The resulting number of edges. Overridden by -p/--probability.
small-world
Description

The small-world topology described in the Watts-Strogatz model.

Specific Arguments
  • -l/--lattice: The dimension of a starting network lattice upon which the Watts-Strogatz model will be applied to generate the small-world. Default is 2. NOTE: It is highly recommended to use small values, as lattices spread across multiple dimensions may create critical memory issues.
  • -s/--lattice-size: Size of the lattice among all dimensions. Default is 2. NOTE: It is highly recommended to use small values, as lattices spread across multiple dimensions may create critical memory issues.
  • --nei: The maximum distance in which two nodes will be connected. Default is arandom integer between 2 and 5.
  • -p/--probability: Rewiring probability. Default is .0.5.
scale-free
Description

The scale-free topology according to the model proposed by Barabási and Albert.

Specific Arguments
  • -n/--nodes: Number of vertices of the resulting scale-free network. If not specified, it will be a number between 100 and 500 (chosen randomly).
  • -a/--avg-edges: Average number of node neighbours for each vertex in the scale-free network.If not specified, it will be a number between 10 and 100 (chosen randomly).
tree
Description

A hierarchical tree network, as described here.

Specific Arguments
  • -n/--nodes: Number of vertices of the resulting tree graph. If not specified, it will be a number between 100 and 500 (chosen randomly)
  • -c/--children: The number of children nodes per parent. If not specified, will be a number between 2 and 10 (chosen randomly).

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test
Description

Performs a series of tests to check Pyntacle integrity. Useful after installing pyntacle and for debugging purposes.


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Usage Example

pyntacle test


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