From 07f02f0511df9895c01a8b06f4a44e0eed232b26 Mon Sep 17 00:00:00 2001 From: Marcin Magnus Date: Tue, 20 Oct 2015 17:41:27 +0200 Subject: [PATCH] Fix - now mutpos are generated from rdata even if you happen to have `mutation:X1X` etc. & it seems to be faster anyway Before: >> output_Zscore_from_rdat('out.txt', 'RNAPZ14_1M7_0000.rdat') Parsing file from rdat: RNAPZ14_1M7_0000.rdat Number of reactivity lines: 59 mutpos (1 x 59) is generated from d_rdat.data_annotations. Subscript indices must either be real positive integers or logicals. Error in output_Zscore_from_rdat>get_Zscore_and_apply_filter (line 219) Zscore_full( pos1, pos2(gp) ) = Zscore(:,gp) * ZSCORE_SCALING; Error in output_Zscore_from_rdat (line 67) [ Z, mutpos ] = get_Zscore_and_apply_filter( d, d_nomod, MEAN_EXPOSURE_CUTOFF, ZSCORE_OFFSET, APPLY_ZSCORE_OFFSET, ONLY_A_C, ignore_mut ); now you will get the plot! Signed-off-by: Marcin Magnus & Filip Ciepiela --- .../graphics/t47_graphics/tool/generate_mutpos_from_rdat.m | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Scripts/utility/graphics/t47_graphics/tool/generate_mutpos_from_rdat.m b/Scripts/utility/graphics/t47_graphics/tool/generate_mutpos_from_rdat.m index 21cb36b..007c149 100644 --- a/Scripts/utility/graphics/t47_graphics/tool/generate_mutpos_from_rdat.m +++ b/Scripts/utility/graphics/t47_graphics/tool/generate_mutpos_from_rdat.m @@ -12,9 +12,10 @@ mutpos = ones(1, size(cell_array, 2)) * NaN; for i = 2:size(mutpos, 2) - mutpos_inferred = str2num(strrep(strrep(strrep(strrep(strrep(cell_array{i}{1}, 'mutation:', ''), 'G', ''), 'A', ''), 'C', ''), 'U', '')); + %mutpos_inferred = str2num(strrep(strrep(strrep(strrep(strrep(strrep(cell_array{i}{1}, 'mutation:', ''), 'G', ''), 'A', ''), 'C', ''), 'U', ''),'X','')); + mutpos_inferred = str2num(regexprep(cell_array{i}{1},'\D','')); if ~isempty( mutpos_inferred ) mutpos(i) = mutpos_inferred; end end; -fprintf(['mutpos (1 x ', num2str(length(mutpos)), ') is generated from d_rdat.data_annotations.\n']); \ No newline at end of file +fprintf(['mutpos (1 x ', num2str(length(mutpos)), ') is generated from d_rdat.data_annotations.\n']);