将Matlab转换为八度是否有一个containers.Map等效？ [英] Converting Matlab to Octave is there a containers.Map equivalent?
本文介绍了将Matlab转换为八度是否有一个containers.Map等效？的处理方法，对大家解决问题具有一定的参考价值，需要的朋友们下面随着小编来一起学习吧！
问题描述
我试图将 Maia包中的一些matlab代码转换成可以工作的东西与八度。我目前陷入困境，因为其中一个文件对 containers.Map 有几个调用，这显然是尚未用八度音程实现。有没有人有任何想法轻松实现类似的功能，而不需要在八度音阶上做很多额外的工作？感谢您的时间。
函数[adj_direct contig_direct重叠名称longest_path_direct ...
weigth_direct deltafiles deltafiles_ref参考对齐.. 。
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将重叠群组合成一个组合染色体
％
％INPUT
％程序集
％ref_chromosome
％Startnode_name
％ Endnode_name
％可选的默认值
％'z_weigths'[.25 .25 .25 .25]
''clipping_thrs'10
''ref_distance'-10
％ 'ref_quality'1E-5
''max_chromosome_dist'100
''quit_treshold'15
％'ta bu_time'3
''minimum_improvement'-inf
''ref_node_assemblies'所有程序集（慢）
％'endextend'真
％
％
％设定默认值
％常规参数
z_weights = [.25 .25 .25 .25];
clipping_thrs = 10;
mapfilter ='-rq';
alignlen = 75;
ident = 85;
％参考点参数
ref_distance = -10;
ref_quality = 1E-5;
max_chromosome_dist = 100;
％TABU参数
quit_treshold = 15;
tabu_time = 3;
minimum_improvement = -inf;
ref_node_assemblies =程序集;
％从开始和结点向外扩展程序集
endextend = true;
AllowReverse = true;
％如果没有给出开始和结束节点，它们将从平铺
Startnode_name =''确定;
Endnode_name ='';
containment_edge = true;
ref_first = true;
％如果contigs已经与参考对齐，请给出
％deltafile
ReferenceAlignment ='NotYetDoneByMaia';
％获取VARARGIN用户输入
如果长度（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};
案例'ref_quality'
ref_quality = varargin {2};
case'max_chromosome_dist'
max_chromosome_dist = varargin {2};
case'quit_treshold'
quit_treshold = varargin {2};
案例'tabu_time'
tabu_time = varargin {2};
case'minimum_improvement'
minimum_improvement = varargin {2};
case'ref_node_assemblies'
ref_node_assemblies =程序集（varargin {2}，:);
case'extend_ends'
endextend =程序集（varargin {2}，:);
案例'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};
案例'ident'
ident = varargin {2};
否则
错误（['输入'varargin {2}'未知']）;
结束
如果长度（varargin）> 2
varargin = varargin（3：end）;
else
break;
end
end
end
读取输入程序集
程序集名称=程序集（：，1）;
assembly_locs = assemblies（：，2）;
assembly_quality = containers.Map（assemblies（：，1），assemblies（：，3））;
assembly_quality（'reference'）= ref_quality;
％读取用于创建参考节点的输入程序集
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;
％如果只有一个程序集，如果size（程序集，1）> = 2
％对齐程序集没有任何对齐
的程序集相互对立
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}}，{程序集名称{i}，程序集名称{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.\\\
'）;
％load alignments_done;
％将nucmer对齐放置在相邻矩阵中
％[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）;
％合并deltafiles
deltafilesnew = deltafiles {1};
if size（deltafiles，1）> 1
for di = 2：size（deltafiles，1）
deltafilesnew = [deltafilesnew deltafiles {di}];
结束
结束
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'，[]）
结束
％将伪节点添加到图中。如果重叠群已经与参考基因组相匹配，那么只要选择与目标染色体
对应的
％对应的比对，如果isequal（ReferenceAlignment，'NotYetDoneByMaia'）
％ 'contig_sets_fasta'中的所有重叠群与参考染色体
[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
％仅选择delta文件中当前目标染色体的条目
[contig_target_ref，overlap_target_ref，name_hash_target_ref，delta_target_ref] = ...
GetVariablesForTargetChromosome（...
contig_ref，overlap_ref，deltafiles_ref）;
％如果平铺
％，参考剪裁应该很高if isqual（max_chromosome_dist，'tiling'）
％clipping_thrs = 10000
％end
％将参考节点添加到相邻矩阵
[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）;
％给参考边缘一些小的额外值来区分参考节点导致的
％程序集之间的区别bb b％adj = rank_reference_edges（adj，contig，assembly_quality） ;
％指定程序集的开始和结束节点
Startnode = name_hash（Startnode_name）;
Endnode = name_hash（Endnode_name）;
％找到最佳得分路径
fprintf（'指导最终图形\'）;
％计算无向图上的路径以获得关于如何指导图的想法
[longest_path weigth] = longest_path_tabu（adj，Startnode，Endnode，quit_treshold，tabu_time，minimum_improvement）;
％使图形指向（贪婪）
[adj_direct contig_direct] = direct_graph（adj，overlap，contig，names，name_hash，clipping_thrs，Startnode，longest_path，true，ref_first）;
％Calcultate最终布局路径
fprintf（'查找最高得分路径\'）;
[longest_path_direct weigth_direct] = longest_path_tabu（adj_direct，Startnode，Endnode，quit_treshold，tabu_time，minimum_improvement）;
函数[contig_target_ref，overlap_target_ref，name_hash_target_ref，delta_target_ref] = ...
GetVariablesForTargetChromosome（...
contig_ref，overlap_ref，deltafiles_ref）
％仅选择delta文件中当前目标染色体的条目
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）= [];
结束
结束
overlap_target_ref = overlap_ref;如果〜isequal（overlap_target_ref（oi）.R，target_chromosome）
overlap_target_ref（oi）= [];
结束
结束
contig_target_ref = contig_ref;
for ci = size（contig_target_ref，1）： - 1：1
if isequal（contig_target_ref（ci）.assembly，'reference'）&& 〜coneg_target_ref（ci）= [];
end
end
name_hash_target_ref = make_hash（{contig_target_ref.name}'）;
end
end
解决方案
在Octave中并没有完全等价的
在Octave中并没有完全等价的
containers.Map 一种选择是使用 java包创建 java。 util.Hashtable 。使用此示例：
pkg load java
d = javaObject（java.util.Hashtable）;
d.put（'a'，1）
d.put（'b'，2）
d.put（'c'，3）
d.get 'b'）
如果您愿意有一点重写，你可以使用内建的 struct 作为一个基本的散列表，字符串（有效变量名）作为关键字，以及存储在值中的任何东西。
例如，给定以下内容：
keys = {'Mon'， 'Tue'，'Wed'}
values = {10,20,30}
你可以替换它：
map = containers.Map（keys，values）;
map（'Mon'）
by：
s = struct（）;
for i = 1：numel（keys）
s。（keys {i}）= values {i};
end
。（'Mon'）
您可能需要使用 genvarname 来产生有效的密钥，或者是一个合适的哈希函数来产生有效的密钥字符串。
相关函数：getfield，setfield，isfield，fieldnames，rmfield等。
I am trying to convert some matlab code from the Maia package into something that will work with Octave. I am currently getting stuck because one of the files has several calls to containers.Map which is apparently something that has not yet been implemented in octave. Does anyone have any ideas for easily achieving similar functionality without doing a whole lot of extra work in octave? Thanks all for your time.
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
解决方案
There is no exact equivalent of containers.Map in Octave that I know of...
One option is to use the java package to create java.util.Hashtable. Using this example:
pkg load java
d = javaObject("java.util.Hashtable");
d.put('a',1)
d.put('b',2)
d.put('c',3)
d.get('b')
If you are willing to do a bit of rewriting, you can use the builtin struct as a rudimentary hash table with strings (valid variable names) as keys, and pretty much anything stored in values.
For example, given the following:
keys = {'Mon','Tue','Wed'}
values = {10, 20, 30}
you could replace this:
map = containers.Map(keys,values);
map('Mon')
by:
s = struct();
for i=1:numel(keys)
s.(keys{i}) = values{i};
end
s.('Mon')
You might need to use genvarname to produce valid keys, or maybe a proper hashing function that produces valid key strings.
Also look into struct-related functions: getfield, setfield, isfield, fieldnames, rmfield, etc..
这篇关于将Matlab转换为八度是否有一个containers.Map等效？的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
查看全文
