source: branches/lib/HELP_SOURCE/source/csp_2_gnuplot.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.3 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Export Column statistics to GnuPlot
12
13OCCURRENCE      ARB_NT/SAI/Etc/Export Column statistics to GnuPlot
14
15DESCRIPTION
16
17        - Select a valid column statistic
18
19        - Select what kind of information should be extracted
20
21             Information         Formula
22             -------------------------------------
23             G+C ratio           (G+C) / N
24             G+A ratio           (G+A) / N
25             Rate                mutation_sum / frequency_sum
26             TT ratio            (min.mutations + transversions) / transversions
27             Most freq. base     F1 / N
28             2nd freq. base      F2 / N
29             3rd freq. base      F3 / N
30             Least freq. base    F4 / N
31             A ratio             A / N
32             C ratio             C / N
33             G ratio             G / N
34             TU ratio            (T+U) / N
35             Helix               boolean (helix or not helix)
36
37             Legend:
38             -------
39             A/C/G/T/U = amount of A/C/G/T/U's in each column
40             N         = total amount of bases in each column
41             Fx        = F1 = count of most freq. base, ..., F4 of least freq. base
42
43
44        - Select if you like smoothing of the values (before they are written to file)
45          '1' means no smoothing, '2' means each value is smoothed with its neighbor, etc.
46          If you e.g. smooth by '21', then the statistic will contain 20 columns less than
47          the unsmoothed stat (for each 21-tupel only one value is written, i.e. 10 values are
48          missing on the left and 10 are missing on the right side).
49
50        - Select a filter
51
52        - Select a filename (specify without extension, which will be appended by ARB)
53
54        - Press 'Save' to save to a file or
55          Press 'Save & View' to save and start gnuplot
56
57          In the last case you have some more options:
58
59             - Select gnuplot-internal smoothing function
60
61             - Select if to overlay other statistics (which were saved before)
62
63NOTES           Pressing 'Delete all overlayed files' will delete all the files, which would be
64                overlayed, if you press 'Save & View'.
65
66EXAMPLES        None
67
68WARNINGS        None
69
70BUGS            No bugs known
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