| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | #Please insert subtopic references (line starts with keyword SUB) |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 9 | |
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| 10 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 11 | TITLE Export Column statistics to GnuPlot |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT/SAI/Etc/Export Column statistics to GnuPlot |
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| 14 | |
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| 15 | DESCRIPTION |
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| 16 | |
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| 17 | - Select a valid column statistic |
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| 18 | |
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| 19 | - Select what kind of information should be extracted |
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| 20 | |
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| 21 | Information Formula |
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| 22 | ------------------------------------- |
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| 23 | G+C ratio (G+C) / N |
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| 24 | G+A ratio (G+A) / N |
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| 25 | Rate mutation_sum / frequency_sum |
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| 26 | TT ratio (min.mutations + transversions) / transversions |
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| 27 | Most freq. base F1 / N |
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| 28 | 2nd freq. base F2 / N |
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| 29 | 3rd freq. base F3 / N |
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| 30 | Least freq. base F4 / N |
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| 31 | A ratio A / N |
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| 32 | C ratio C / N |
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| 33 | G ratio G / N |
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| 34 | TU ratio (T+U) / N |
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| 35 | Helix boolean (helix or not helix) |
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| 36 | |
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| 37 | Legend: |
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| 38 | ------- |
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| 39 | A/C/G/T/U = amount of A/C/G/T/U's in each column |
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| 40 | N = total amount of bases in each column |
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| 41 | Fx = F1 = count of most freq. base, ..., F4 of least freq. base |
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| 42 | |
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| 43 | |
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| 44 | - Select if you like smoothing of the values (before they are written to file) |
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| 45 | '1' means no smoothing, '2' means each value is smoothed with its neighbor, etc. |
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| 46 | If you e.g. smooth by '21', then the statistic will contain 20 columns less than |
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| 47 | the unsmoothed stat (for each 21-tupel only one value is written, i.e. 10 values are |
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| 48 | missing on the left and 10 are missing on the right side). |
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| 49 | |
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| 50 | - Select a filter |
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| 51 | |
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| 52 | - Select a filename (specify without extension, which will be appended by ARB) |
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| 53 | |
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| 54 | - Press 'Save' to save to a file or |
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| 55 | Press 'Save & View' to save and start gnuplot |
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| 56 | |
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| 57 | In the last case you have some more options: |
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| 58 | |
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| 59 | - Select gnuplot-internal smoothing function |
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| 60 | |
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| 61 | - Select if to overlay other statistics (which were saved before) |
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| 62 | |
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| 63 | NOTES Pressing 'Delete all overlayed files' will delete all the files, which would be |
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| 64 | overlayed, if you press 'Save & View'. |
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| 65 | |
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| 66 | EXAMPLES None |
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| 67 | |
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| 68 | WARNINGS None |
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| 69 | |
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| 70 | BUGS No bugs known |
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