This is a static copy of a profile report

Home

Load_genome_information (2 calls, 0.171 sec)
Generated 14-Nov-2016 07:47:08 using cpu time.
function in file /home/user/dev/ymap/scripts_seqModules/Load_genome_information.m
Copy to new window for comparing multiple runs

Parents (calling functions)

Function NameFunction TypeCalls
LOH_hapmap_v4function1
allelic_ratios_WGseqfunction1
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
182
figure_details(lines_analyzed)...
160.020 s11.8%
177
end;
8540.020 s11.8%
220
currentChrSize          = chrS...
160.010 s5.9%
212
if (strcmp(figure_details(i).w...
160.010 s5.9%
209
fprintf([num2str(figure_detail...
160.010 s5.9%
All other lines  0.101 s58.8%
Totals  0.171 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
num2strfunction640.030 s17.6%
str2doublefunction1440.020 s11.8%
str2numfunction280 s0%
fgetlfunction580 s0%
Self time (built-ins, overhead, etc.)  0.121 s70.6%
Totals  0.171 s100% 
Code Analyzer results
Line numberMessage
10The value assigned to variable 'discard' might be unused.
26The variable 'centromeres' appears to change size on every loop iteration. Consider preallocating for speed.
27The variable 'centromeres' appears to change size on every loop iteration. Consider preallocating for speed.
28The variable 'centromeres' appears to change size on every loop iteration. Consider preallocating for speed.
33Using ISEMPTY is usually faster than comparing LENGTH to 0.
43The value assigned to variable 'discard' might be unused.
59The variable 'chrSize' appears to change size on every loop iteration. Consider preallocating for speed.
60The variable 'chrSize' appears to change size on every loop iteration. Consider preallocating for speed.
61The variable 'chrSize' appears to change size on every loop iteration. Consider preallocating for speed.
65Using ISEMPTY is usually faster than comparing LENGTH to 0.
75The value assigned to variable 'discard' might be unused.
114The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
115The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
116The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
117The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
118The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
119The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
120The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
121The variable 'annotations' appears to change size on every loop iteration. Consider preallocating for speed.
139The value assigned to variable 'discard' might be unused.
153If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
154If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
155If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
156If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
178The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
179The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
180The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
181The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
182The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
183The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
184The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
185The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
186If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
191If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
195Using ISEMPTY is usually faster than comparing LENGTH to 0.
213If you are operating on scalar values, consider using STR2DOUBLE for faster performance.
221The variable 'figure_details' appears to change size on every loop iteration. Consider preallocating for speed.
Coverage results
Show coverage for parent directory
Total lines in function226
Non-code lines (comments, blank lines)34
Code lines (lines that can run)192
Code lines that did run136
Code lines that did not run56
Coverage (did run/can run)70.83 %
Function listing
time 
calls 
 line
   1 
function [centromeres, chrSize, figure_details, annotations, figInfo_ploidy_default] = Load_genome_information(genomeDir)
      2 
   2 
fprintf(['\nLoad_genome_information_1.m : Genome in use : [' genomeDir ']\n']); 
   3 

   4 
% Load centromere definition file.
   5 
%    This is text file containing one header line and two columns.
   6 
%    The two columns hold the start and end bp for the centromeres, with
   7 
%       respect to each chromosome.
      2 
   8 
centromeres          = []; 
      2 
   9 
centromere_fid       = fopen([genomeDir 'centromere_locations.txt'], 'r'); 
      2 
  10 
discard              = fgetl(centromere_fid); 
      2 
  11 
lines_analyzed       = 0; 
      2 
  12 
fprintf(['\t' genomeDir '/centromere_locations.txt\n']); 
      2 
  13 
while not (feof(centromere_fid)) 
     16 
  14 
	lineData       = fgetl(centromere_fid); 
     16 
  15 
	lines_analyzed = lines_analyzed+1; 
     16 
  16 
	cen_chr        = sscanf(lineData, '%s',1); 
     16 
  17 
	cen_start      = sscanf(lineData, '%s',2); 
     16 
  18 
	for i = 1:size(sscanf(lineData,'%s',1),2); 
     16 
  19 
		cen_start(1) = []; 
     16 
  20 
	end; 
     16 
  21 
	cen_end   = sscanf(lineData, '%s',3); 
     16 
  22 
	for i = 1:size(sscanf(lineData,'%s',2),2); 
     32 
  23 
		cen_end(1) = []; 
     32 
  24 
	end; 
  0.01 
     16 
  25 
	chr = str2double(cen_chr); 
     16 
  26 
	centromeres(chr).chr   = chr; 
     16 
  27 
	centromeres(chr).start = str2double(cen_start); 
     16 
  28 
	centromeres(chr).end   = str2double(cen_end); 
  0.01 
     16 
  29 
	fprintf(['\t\t|' lineData '\n']); 
     16 
  30 
end; 
      2 
  31 
fclose(centromere_fid); 
      2 
  32 
clear cen_start cen_end line lines_analyzed i ans cen_chr centromere_fid chromosome; 
      2 
  33 
if (length(centromeres) == 0) 
  34 
	error('[analyze_CNVs]: Centromere definition file is missing.');
  35 
end;
  36 

  37 
% Load chromosome size definition file.
  38 
%    This is text file containing one header line and two columns.
  39 
%    The two columns hold the start and end bp for the centromeres, with
  40 
%       respect to each chromosome.
      2 
  41 
chrSize        = []; 
  0.01 
      2 
  42 
chrSize_fid    = fopen([genomeDir '/chromosome_sizes.txt'],'r'); 
      2 
  43 
discard        = fgetl(chrSize_fid); 
      2 
  44 
lines_analyzed = 0; 
      2 
  45 
fprintf(['\t' genomeDir '/chromosome_sizes.txt\n']); 
      2 
  46 
while not (feof(chrSize_fid)) 
     16 
  47 
	lineData          = fgetl(chrSize_fid); 
     16 
  48 
	lines_analyzed    = lines_analyzed+1; 
     16 
  49 
	size_chr          = sscanf(lineData, '%s',1); 
     16 
  50 
	size_size         = sscanf(lineData, '%s',2); 
     16 
  51 
	for i = 1:size(sscanf(lineData,'%s',1),2); 
     16 
  52 
		size_size(1) = []; 
     16 
  53 
	end; 
     16 
  54 
	size_name         = sscanf(lineData, '%s',3); 
     16 
  55 
	for i = 1:size(sscanf(lineData,'%s',2),2); 
    126 
  56 
		size_name(1) = []; 
    126 
  57 
	end; 
     16 
  58 
	chr               = str2double(size_chr); 
     16 
  59 
	chrSize(chr).chr  = chr; 
  0.01 
     16 
  60 
	chrSize(chr).size = str2double(size_size); 
     16 
  61 
	chrSize(chr).name = size_name; 
     16 
  62 
	fprintf(['\t\t|' lineData '\n']); 
     16 
  63 
end; 
      2 
  64 
fclose(chrSize_fid); 
      2 
  65 
if (length(chrSize) == 0) 
  66 
	error('[analyze_CNVs]: Chromosome size definition file is missing.');
  67 
end;
  68 

  69 
% Load additional annotation location definition file.
  70 
%    This is text file containing one header line and two columns.
  71 
%    The two columns hold the start and end bp for the centromeres, with
  72 
%       respect to each chromosome.
      2 
  73 
annotations       = []; 
      2 
  74 
annotations_fid   = fopen([genomeDir '/annotations.txt'], 'r'); 
      2 
  75 
discard           = fgetl(annotations_fid); 
      2 
  76 
lines_analyzed    = 0; 
      2 
  77 
annotations_count = 0; 
      2 
  78 
fprintf(['\t' genomeDir '/annotations.txt\n']); 
      2 
  79 
while not (feof(annotations_fid)) 
  80 
	lineData = fgetl(annotations_fid);
  81 
	if (strcmp(lineData(1),'#') == 0)
  82 
		lines_analyzed    = lines_analyzed+1;
  83 
		annotations_chr   = sscanf(lineData, '%s',1);
  84 
		annotations_type  = sscanf(lineData, '%s',2);
  85 
		for i = 1:size(sscanf(lineData,'%s',1),2);
  86 
			annotations_type(1) = [];
  87 
		end;
  88 
		annotations_start = sscanf(lineData, '%s',3);
  89 
		for i = 1:size(sscanf(lineData,'%s',2),2);
  90 
			annotations_start(1) = [];
  91 
		end;
  92 
		annotations_end   = sscanf(lineData, '%s',4);
  93 
		for i = 1:size(sscanf(lineData,'%s',3),2);
  94 
			annotations_end(1) = [];
  95 
		end;
  96 
		annotations_name  = sscanf(lineData, '%s',5);
  97 
		for i = 1:size(sscanf(lineData,'%s',4),2);
  98 
			annotations_name(1) = [];
  99 
		end;
 100 
		annotations_fillcolor  = sscanf(lineData, '%s',6);
 101 
		for i = 1:size(sscanf(lineData,'%s',5),2);
 102 
			annotations_fillcolor(1) = [];
 103 
		end;
 104 
		annotations_edgecolor  = sscanf(lineData, '%s',7);
 105 
		for i = 1:size(sscanf(lineData,'%s',6),2);
 106 
			annotations_edgecolor(1) = [];
 107 
		end;
 108 
		annotations_size  = sscanf(lineData, '%s',8);
 109 
		for i = 1:size(sscanf(lineData,'%s',7),2);
 110 
			annotations_size(1) = [];
 111 
		end;
 112 

 113 
		annotations_count                        = annotations_count+1;
 114 
		annotations(annotations_count).chr       = str2double(annotations_chr);
 115 
		annotations(annotations_count).type      = annotations_type;
 116 
		annotations(annotations_count).start     = str2double(annotations_start);
 117 
		annotations(annotations_count).end       = str2double(annotations_end);
 118 
		annotations(annotations_count).name      = annotations_name;
 119 
		annotations(annotations_count).fillcolor = annotations_fillcolor;
 120 
		annotations(annotations_count).edgecolor = annotations_edgecolor;
 121 
		annotations(annotations_count).size      = str2double(annotations_size);
 122 
		fprintf(['\t\t|' lineData '\n']);
 123 
	end;
 124 
end;
      2 
 125 
fclose(annotations_fid); 
 126 

 127 
% Load figure definition file.
 128 
% This is text file containing one header line and seven columns.
 129 
%    Chr #      : Numerical designations of chromosomes.   (0 is used for line defining figure key.)
 130 
%    Chr label  : The label to use for identifying the chromosome in the figure.
 131 
%    Chr name   : The full name of the chromosome.
 132 
%    Chr posX   : The X-position in % from left to right.
 133 
%    Chr posY   : The Y-position in % from bottom to top.
 134 
%    Chr width  : The width in %.
 135 
%    Chr height : The height in %.
      2 
 136 
figInfo_ploidy_default = 2.0; 
      2 
 137 
figure_details         = []; 
      2 
 138 
figInfo_fid            = fopen([genomeDir '/figure_definitions.txt'], 'r'); 
      2 
 139 
discard                = fgetl(figInfo_fid); 
      2 
 140 
lines_analyzed         = 0; 
  0.01 
      2 
 141 
fprintf(['\t' genomeDir '/figure_definitions.txt\n']); 
      2 
 142 
while not (feof(figInfo_fid)) 
     18 
 143 
	lineData       = fgetl(figInfo_fid); 
     18 
 144 
	figInfo_chr    = sscanf(lineData, '%s',1); 
     18 
 145 
	figInfo_useChr = sscanf(lineData, '%s',2); 
     18 
 146 
	for i = 1:size(sscanf(lineData,'%s',1),2); 
     18 
 147 
		figInfo_useChr(1) = []; 
     18 
 148 
	end; 
     18 
 149 
	figInfo_label = sscanf(lineData, '%s',3); 
     18 
 150 
	for i = 1:size(sscanf(lineData,'%s',2),2); 
     36 
 151 
		figInfo_label(1) = []; 
     36 
 152 
	end; 
     18 
 153 
	if (str2num(figInfo_chr) > 0) || ... 
 154 
	   (str2num(figInfo_useChr) > 0) || ...
 155 
	   ((str2num(figInfo_chr) == 0) && (strcmp(figInfo_label,'Key') == 1)) || ...
 156 
	   ((str2num(figInfo_chr) == 0) && (strcmp(figInfo_label,'Mito') == 1))
     16 
 157 
		lines_analyzed = lines_analyzed+1; 
     16 
 158 
		figInfo_name   = sscanf(lineData, '%s',4); 
     16 
 159 
		for i = 1:size(sscanf(lineData,'%s',3),2); 
     96 
 160 
			figInfo_name(1) = []; 
     96 
 161 
		end; 
     16 
 162 
		figInfo_posX   = sscanf(lineData, '%s',5); 
     16 
 163 
		for i = 1:size(sscanf(lineData,'%s',4),2); 
  0.01 
    512 
 164 
			figInfo_posX(1) = []; 
  0.01 
    512 
 165 
		end; 
     16 
 166 
		figInfo_posY   = sscanf(lineData, '%s',6); 
     16 
 167 
		for i = 1:size(sscanf(lineData,'%s',5),2); 
    576 
 168 
			figInfo_posY(1) = []; 
    576 
 169 
		end; 
     16 
 170 
		figInfo_width   = sscanf(lineData, '%s',7); 
     16 
 171 
		for i = 1:size(sscanf(lineData,'%s',6),2); 
    834 
 172 
			figInfo_width(1) = []; 
  0.01 
    834 
 173 
		end; 
     16 
 174 
		figInfo_height   = sscanf(lineData, '%s',8); 
     16 
 175 
		for i = 1:size(sscanf(lineData,'%s',7),2); 
    854 
 176 
			figInfo_height(1) = []; 
  0.02 
    854 
 177 
		end; 
     16 
 178 
		figure_details(lines_analyzed).chr    = str2double(figInfo_chr); 
     16 
 179 
		figure_details(lines_analyzed).label  = figInfo_label; 
     16 
 180 
		figure_details(lines_analyzed).name   = figInfo_name; 
     16 
 181 
		figure_details(lines_analyzed).useChr = figInfo_useChr; 
  0.02 
     16 
 182 
		figure_details(lines_analyzed).posX   = str2double(figInfo_posX); 
     16 
 183 
		figure_details(lines_analyzed).posY   = str2double(figInfo_posY); 
     16 
 184 
		figure_details(lines_analyzed).width  = figInfo_width; 
     16 
 185 
		figure_details(lines_analyzed).height = str2double(figInfo_height); 
      2 
 186 
    	elseif ((str2num(figInfo_chr) == 0) && (strcmp(figInfo_label,'Ploidy') == 1)) 
 187 
		figInfo_ploidy_default = sscanf(lineData, '%s',4);
 188 
		for i = 1:size(sscanf(lineData,'%s',3),2);
 189 
			figInfo_ploidy_default(1) = [];
 190 
		end;
 191 
		figInfo_ploidy_default = str2num(figInfo_ploidy_default);
 192 
	end;
     18 
 193 
	fprintf(['\t\t|' lineData '\n']); 
     18 
 194 
end; 
      2 
 195 
if (length(figure_details) == 0) 
 196 
	error('[analyze_CNVs]: Figure display definition file is missing.');
 197 
end;
 198 

 199 
%% figure out widths for chromosomes in figure.
      2 
 200 
maxFigSize = 0; 
      2 
 201 
maxChrSize = 0; 
      2 
 202 
for i = 1:length(figure_details) 
  0.01 
     16 
 203 
	fprintf(['Fig_chr : [' num2str(figure_details(i).chr) '|']); 
     16 
 204 
	fprintf([figure_details(i).label '|']); 
     16 
 205 
	fprintf([figure_details(i).name '|']); 
  0.01 
     16 
 206 
	fprintf([num2str(figure_details(i).posX) '|']); 
     16 
 207 
	fprintf([num2str(figure_details(i).posY) '|']); 
     16 
 208 
	fprintf([figure_details(i).width '|']); 
  0.01 
     16 
 209 
	fprintf([num2str(figure_details(i).height) ']\n']); 
 210 

     16 
 211 
	if (figure_details(i).chr > 0) 
  0.01 
     16 
 212 
		if (strcmp(figure_details(i).width(1),'*') == 0) 
      2 
 213 
			maxFigSize = str2num(figure_details(i).width); 
      2 
 214 
			maxChrSize = chrSize(figure_details(i).chr).size; 
      2 
 215 
		end; 
     16 
 216 
	end; 
     16 
 217 
end; 
      2 
 218 
for i = 1:length(figure_details) 
     16 
 219 
	if (figure_details(i).chr > 0) 
  0.01 
     16 
 220 
		currentChrSize          = chrSize(figure_details(i).chr).size; 
     16 
 221 
		figure_details(i).width = currentChrSize/maxChrSize*maxFigSize; 
     16 
 222 
	end; 
     16 
 223 
end; 
      2 
 224 
fclose(figInfo_fid); 
 225 

      2 
 226 
end