Konvertieren Matlab zu Octave gibt es einen Container. Karte gleichwertig?

Question

Ich versuche, etwas Matlab-Code von Maia package in etwas zu konvertieren, das mit Octave arbeiten wird. Ich stehe derzeit fest, weil eine der Dateien mehrere Aufrufe an containers.Map hat, die anscheinend etwas ist, das not yet been implemented in octave hat. Hat jemand irgendwelche Ideen, um ähnliche Funktionen leicht zu erreichen, ohne eine Menge Extra-Arbeit in der Oktave zu machen? Vielen Dank für Ihre Zeit.

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

Es gibt keine genaue Entsprechung von containers.Map in Octave, die ich kenne ...

Eine Möglichkeit ist es, die java package zu verwenden java.util.Hashtable zu erstellen. dies mit example:

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

---

Wenn Sie bereit sind, ein wenig umschreiben zu tun, können Sie die eingebauten struct als rudimentäre Hash-Tabelle mit Strings (gültige Variablennamen) als Schlüssel verwenden, und so ziemlich alles in Werten gespeichert.

Zum Beispiel angesichts der folgenden:

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

Sie diese ersetzen könnten:

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

von:

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

Sie müssen möglicherweise genvarname verwenden gültige Schlüssel zu erzeugen, oder vielleicht eine richtige Hash-Funktion, die gültige Schlüsselfolgen erzeugt.

Schauen Sie auch in Struktur-bezogene Funktionen: getfield, SetField, Isfield, Feldnamen, rmfield, etc ..