time | calls | line |
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| | 1 | function [] = analyze_SNPs_hapmap(main_dir, user, genomeUser, project, parent_or_hapmap, genome, ploidyEstimateString,ploidyBaseString)
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| | 2 | % analyze_CNVS(<Project Name>,<Project File>,<Ploidy Estimate)
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| | 3 | % A componant of the sequence analysis pipeline, analyzing SNPs only.
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| | 4 | % <Project Name> : the name of the project.
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| | 5 | % <Project File> : the name of the project file, including directory location.
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| | 6 | % <Ploidy Estimate> : a numerical value for ploidy from other work.
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| | 7 |
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| | 8 | % log file start, for in-process analysis.
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| 1 | 9 | fprintf(['project : [[[' project '[[[\n']);
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| | 10 |
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| 1 | 11 | workingDir = [main_dir 'users/' user '/projects/' project '/'];
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| 1 | 12 | figureDir = workingDir;
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| 1 | 13 | CNV_verString = 'v1';
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| 1 | 14 | INDEL_verString = 'v1';
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| 1 | 15 | SNP_verString = 'v4';
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| 1 | 16 | rDNA_verString = 'v1';
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| 1 | 17 | LOH_verString = 'v2';
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| 1 | 18 | displayBREAKS = true;
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| 1 | 19 | referenceCHR = 1;
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| | 20 |
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| | 21 | %% Grab the first column of the first line of the putative_SNP pileup file.
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| 1 | 22 | datafile = [workingDir 'putative_SNPs_' SNP_verString '.txt'];
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| 1 | 23 | data = fopen(datafile);
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| 1 | 24 | fprintf(['datafile : ' datafile]);
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| 1 | 25 | line = fgetl(data); % grab the first line of the putative_CNV datafile.
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| | 26 | % printing first line only if file is not empty
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| 1 | 27 | if (~feof(data))
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| 1 | 28 | fprintf(['\n' datafile '::' num2str(data) '::' line '\n']);
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| 1 | 29 | exampleChrName = sscanf(line, '%s',1); % grab the first column, ex : 'ChrA_C_glabrata_CBS138';
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| | 30 | else
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| | 31 | fprintf('putative_SNPs file is empty');
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| | 32 | end;
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| 1 | 33 | fclose(data);
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| | 34 |
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| | 35 |
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46.61 | 1 | 36 | LOH_hapmap_v4(main_dir,user,genomeUser,project,parent_or_hapmap,genome,ploidyEstimateString,ploidyBaseString,SNP_verString,LOH_verString,CNV_verString,displayBREAKS);
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| | 37 |
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| 1 | 38 | parent = parent_or_hapmap;
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| 1 | 39 | hapmap = parent_or_hapmap;
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792.31 | 1 | 40 | allelic_ratios_WGseq(main_dir,user,genomeUser,project,parent,hapmap,genome,ploidyEstimateString,ploidyBaseString,SNP_verString,LOH_verString,CNV_verString,displayBREAKS);
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| | 41 |
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| | 42 |
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| 1 | 43 | fprintf('*--- End of ''analyze_SNPs.m'' was reached. ---*\n');
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| 1 | 44 | end
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