Convirtiendo Matlab en Octave ¿hay un contenedor.Mapa equivalente?

Question

Estoy intentando convertir algún código de matlab del Maia package en algo que funcione con Octave. Actualmente me estoy atascando porque uno de los archivos tiene varias llamadas al containers.Map que aparentemente es algo que tiene not yet been implemented in octave. ¿Alguien tiene alguna idea para lograr fácilmente una funcionalidad similar sin hacer mucho trabajo extra en octava? Gracias a todos por su tiempo.

function [adj_direct contig_direct overlap names longest_path_direct... 
      weigth_direct deltafiles deltafiles_ref ReferenceAlignment ... 
      contig_ref overlap_ref name_hash_ref] = ... 
      assembly_driver(assemblies,ref_genome,target_chromosome, ... 
          deltafiles_ref,contig_ref, overlap_ref, ... 
          name_hash_ref, varargin) 

% ASSEMBLY_DRIVER Combines contig sets into one assembled chromosome 
% 
% INPUT 
% assemblies 
% ref_chromosome 
% Startnode_name 
% Endnode_name 
%  OPTIONAL    DEFAULT 
%  'z_weigths'   [.25 .25 .25 .25] 
%  'clipping_thrs'  10 
%  'ref_distance'   -10 
%  'ref_quality'   1E-5 
%  'max_chromosome_dist' 100 
%  'quit_treshold'  15 
%  'tabu_time'   3 
%  'minimum_improvement' -inf 
%  'ref_node_assemblies' all assemblies (slow) 
%  'endextend'   true 
% 
% 

    % SET DEFAULTS 
    % General parameters 
    z_weights   = [.25 .25 .25 .25]; 
    clipping_thrs  = 10; 
    mapfilter   = '-rq'; 
    alignlen   = 75; 
    ident    = 85; 

    % Reference nod parameters 
    ref_distance  = -10; 
    ref_quality   = 1E-5; 
    max_chromosome_dist = 100; 
    % TABU parameters 
    quit_treshold  = 15; 
    tabu_time   = 3; 
    minimum_improvement = -inf; 
    ref_node_assemblies = assemblies; 
    % Extending the assembly outwards from the start and en node 
    endextend   = true; 
    AllowReverse  = true; 
    % If no start and end node are given, they will be determined from tiling 
    Startnode_name  = ''; 
    Endnode_name  = ''; 
    containment_edge = true; 
    ref_first   = true; 

    % If contigs have already been aligned to the reference, give the 
    % deltafile 
    ReferenceAlignment = 'NotYetDoneByMaia'; 

    % Get VARARGIN user input 
    if length(varargin) > 0 
     while 1 
      switch varargin{1} 
       case 'Startnode_name' 
        Startnode_name = varargin{2}; 
       case 'Endnode_name' 
        Endnode_name = varargin{2}; 
       case 'z_weigths' 
        z_weights = varargin{2}; 
       case 'clipping_thrs' 
        clipping_thrs = varargin{2}; 
       case 'ref_distance' 
        ref_distance = varargin{2}; 
       case 'ref_quality' 
        ref_quality = varargin{2}; 
       case 'max_chromosome_dist' 
        max_chromosome_dist = varargin{2}; 
       case 'quit_treshold' 
        quit_treshold = varargin{2}; 
       case 'tabu_time' 
        tabu_time = varargin{2}; 
       case 'minimum_improvement' 
        minimum_improvement = varargin{2}; 
       case 'ref_node_assemblies' 
        ref_node_assemblies = assemblies(varargin{2},:); 
       case 'extend_ends' 
        endextend = assemblies(varargin{2},:); 
       case 'AllowReverse' 
        AllowReverse = varargin{2}; 
       case 'ReferenceAlignment' 
        ReferenceAlignment = varargin{2}; 
       case 'containment_edge' 
        containment_edge = varargin{2}; 
       case 'ref_first' 
        ref_first = varargin{2}; 
       case 'mapfilter' 
        mapfilter = varargin{2}; 
       case 'alignlen' 
        alignlen = varargin{2}; 
       case 'ident' 
        ident = varargin{2}; 
       otherwise 
        error(['Input ' varargin{2} ' is not known']); 
      end 
      if length(varargin) > 2 
       varargin = varargin(3:end); 
      else 
       break; 
      end 
     end 
    end 

    % Read input assemblies 
    assembly_names = assemblies(:,1); 
    assembly_locs = assemblies(:,2); 
    assembly_quality = containers.Map(assemblies(:,1),assemblies(:,3)); 
    assembly_quality('reference') = ref_quality; 

    % Read input assemblies for creation of reference nodes 
    ref_node_assembly_names = ref_node_assemblies(:,1); 
    ref_node_assembly_locs = ref_node_assemblies(:,2); 
    ref_node_assembly_quality = containers.Map(ref_node_assemblies(:,1),ref_node_assemblies(:,3)); 
    ref_node_assembly_quality('reference') = ref_quality; 


    % If there is only one assembly there is nothing to align 
    if size(assemblies,1) >= 2 

     % Align assemblies against each other 
     assembly_pairs = {}; 
     coordsfiles = []; 
     deltafiles = []; 
     for i = 1:length(assembly_locs)-1 
      for j = i+1:length(assembly_locs) 
       [coordsfile,deltafile] = align_assemblies({assembly_locs{i},assembly_locs{j}},{assembly_names{i}, assembly_names{j}}, ... 
                  mapfilter, alignlen, ident); 
       coordsfiles = [coordsfiles; coordsfile]; 
       %deltafiles = [deltafiles deltafile]; 
       deltafiles = [deltafiles; {deltafile}]; 
       assembly_pairs = [assembly_pairs;[assembly_names(i) assembly_names(j)]]; 
      end 
     end 


    % fprintf('Loading alignment files.\n'); 
    % load alignments_done; 

     % Put the nucmer alignments in an adjency matrix 
     %[adj, names, name_hash, contig, overlap] = get_adj_matrix(coordsfiles, assembly_pairs, assembly_quality, z_weights, 'clipping_thrs', clipping_thrs, 'dove_tail', 'double','edge_weight','z-scores', 'containment_edge', true); 
     [adj, names, name_hash, contig, overlap] = get_adj_matrix(deltafiles, assembly_pairs, assembly_quality, z_weights, 'clipping_thrs', clipping_thrs, 'dove_tail', 'double','edge_weight','z-scores', 'containment_edge', containment_edge); 



     % Merge deltafiles 
     deltafilesnew = deltafiles{1}; 
     if size(deltafiles,1) > 1 
      for di = 2:size(deltafiles,1) 
       deltafilesnew = [deltafilesnew deltafiles{di}]; 
      end 
     end 
     deltafiles = deltafilesnew; 

    else 
     assembly_pairs = {}; 
     coordsfiles = []; 
     deltafiles = [];   
     adj = []; 
     names = {}; 
     name_hash = containers.Map; 
     contig = struct('name',{},'size',[],'chromosome',[],'number',[], 'assembly', [], 'assembly_quality', []); 
     overlap = struct('Q',{},'R',[],'S1',[],'E1', [], 'S2', [], 'E2', [], 'LEN1', [], 'LEN2', [], 'IDY', [], 'COVR', [], 'COVQ', [],'LENR',[], 'LENQ',[]); 
    end 


    % Ad the pseudo nodes to the graph. If the contigs have already been 
    % aligned to the reference genome, just select the alignments that 
    % correspond to the target chromosome 
    if isequal(ReferenceAlignment,'NotYetDoneByMaia') 
     % Align all contigs in 'contig_sets_fasta' to the reference chromosome 
     [contig_ref, overlap_ref, name_hash_ref, deltafiles_ref] = align_contigs_sets(... 
      ref_genome, ref_node_assembly_locs, ref_node_assembly_names, ... 
      ref_node_assembly_quality, clipping_thrs, z_weights, ... 
      ref_distance,max_chromosome_dist); 

     ReferenceAlignment = 'out2.delta'; 
    end 
    % Select only the entries in the deltafile for the current target chromosome 
    [contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref] = ... 
       GetVariablesForTargetChromosome(... 
       contig_ref, overlap_ref, deltafiles_ref); 


    % Ref clipping should be high in case of tiling 
    %if isequal(max_chromosome_dist,'tiling') 
    % clipping_thrs = 10000 
    %end 

    % Add reference nodes to the adjency matrix 
    [adj, names, name_hash, contig, overlap, delta_target_ref, Startnode_name, Endnode_name] = get_reference_nodes(... 
        adj, names, name_hash, contig, overlap, target_chromosome, ... 
        contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref, ... 
        max_chromosome_dist, ref_distance, clipping_thrs, ref_first,... 
        Startnode_name, Endnode_name, AllowReverse); 


    % Give reference edges some small extra value to distict between 
    % assemblies to which a reference node leads 
    % adj = rank_reference_edges(adj,contig,assembly_quality); 

    % Specify a start and an end node for the assembly 
    Startnode = name_hash(Startnode_name); 
    Endnode = name_hash(Endnode_name); 


    % Find the best scoring path 
    fprintf('Directing the final graph\n'); 
    % Calculate path on undirected graph to get an idea on how to direct the graph 
    [longest_path weigth] = longest_path_tabu(adj, Startnode, Endnode, quit_treshold, tabu_time, minimum_improvement); 
    % Make the graph directed (greedy) 
    [adj_direct contig_direct] = direct_graph(adj,overlap, contig, names, name_hash,clipping_thrs, Startnode, longest_path, true, ref_first); 
    % Calcultate final layout-path 
    fprintf('Find highest scoring path\n'); 
    [longest_path_direct weigth_direct] = longest_path_tabu(adj_direct, Startnode, Endnode, quit_treshold, tabu_time, minimum_improvement); 


    function [contig_target_ref, overlap_target_ref, name_hash_target_ref, delta_target_ref] = ... 
       GetVariablesForTargetChromosome(... 
       contig_ref, overlap_ref, deltafiles_ref) 

     % Select only the entries in the deltafile for the current target chromosome 
     delta_target_ref = deltafiles_ref; 
     for di = size(delta_target_ref,2):-1:1 
      if ~isequal(delta_target_ref(di).R,target_chromosome) 
       delta_target_ref(di) = []; 
      end 
     end 
     overlap_target_ref = overlap_ref; 
     for oi = size(overlap_target_ref,2):-1:1 
      if ~isequal(overlap_target_ref(oi).R,target_chromosome) 
       overlap_target_ref(oi) = []; 
      end 
     end  
     contig_target_ref = contig_ref; 
     for ci = size(contig_target_ref,1):-1:1 
      if isequal(contig_target_ref(ci).assembly, 'reference') && ~isequal(contig_target_ref(ci).name,target_chromosome) 
       contig_target_ref(ci) = []; 
      end 
     end  
     name_hash_target_ref = make_hash({contig_target_ref.name}'); 
    end 


end 

Answer 1

No hay un equivalente exacto de containers.Map en Octave, que yo sepa ...

Una opción es utilizar el java package para crear java.util.Hashtable. El uso de este example:

pkg load java 
d = javaObject("java.util.Hashtable"); 
d.put('a',1) 
d.put('b',2) 
d.put('c',3) 
d.get('b') 

---

Si usted está dispuesto a hacer un poco de volver a escribir, puede utilizar la orden interna struct como una mesa rudimentaria hash con cuerdas (nombres de variables válidos) como claves, y casi cualquier cosa almacenado en valores

Por ejemplo, dada la siguiente:

keys = {'Mon','Tue','Wed'} 
values = {10, 20, 30} 

podría reemplazar esto:

map = containers.Map(keys,values); 
map('Mon') 

por:

s = struct(); 
for i=1:numel(keys) 
    s.(keys{i}) = values{i}; 
end 
s.('Mon') 

Es posible que necesite usar genvarname para producir las claves válidas, o tal vez una función de hash adecuada que produce cadenas de teclas válidas.

también se ven en las funciones relacionadas con struct-: getField, setField, isfield, nombres de campos, rmfield, etc ..