gff2aplot - Converting GFF files for pairwise alignments to
PostScript.
gff2aplot [options] <GFF_files|STDIN>
This manual page documents briefly the gff2aplot
command.
gff2aplot is a program that draws color-filled alignment
plots from GFF files for that alignment and two sequences annotations.
A double dash on itself "--" signals end of the options
and start of file names (if present). You can use a single dash
"-" as STDIN placeholder. Available options and a short
description are listed here:
- -h, --help
- Show summary of options.
- --version
- Shows current version and exits.
- -v, --verbose
- Verbose mode, a full report is sent to standard error (default is set to
showing only WARNINGS).
- -V, --logs-filename
<filename>
- Report is written to a log file.
- -q, --quiet
- Quiet mode, do not show any message/warning to standard error (reporting
only ERRORS).
- -p, --page-size
<format_name>
- Setting a page size among pre-defined ones see below for a list of
available page formats).
- --margin-left
<length>
- --margin-right
<length>
- --margin-top
<length>
- --margin-bottom
<length>
- Setting each page margin to <length>. If no units are provided,
points are assumed, you can use points, milimeters, centimeters or inches
(pt, mm, cm or in, respectively).
- -B, --background-color
<color>
- Background color.
- -F, --foreground-color
<color>
- Foreground color.
- -T, --title
<string>
- Definning plot title.
- -t, --subtitle
<string>
- Definning plot subtitle.
- -X, --x-label
<string>
- Defining X-axis label.
- -Y, --y-label
<Y-Label>
- Defining Y-axis label.
- -L, --percent-box-label
<string>
- Defining percent-box label.
- -l, --extra-box-label
<XBox-Label>
- Definning Extra-Box Label.
- -x, --x-sequence-coords
<pos..pos>
- -S, --start-x-sequence
<pos>
- Sets X-sequence first nucleotide.
- -E, --end-x-sequence
<pos>
- Sets X-sequence last nucleotide.
- -y, ---y-sequence-coords
<pos..pos>
- -s, --start-y-sequence
<pos>
- Sets Y-sequence first nucleotide.
- -e, --end-y-sequence
<pos>
- Sets Y-sequence last nucleotide.
- --x-sequence-zoom
<pos..pos>
- --y-sequence-zoom
<pos..pos>
- -Z, --zoom [ [-S <pos>]
[-E <pos>] [-s <pos>] [-e <pos>] ]
- This option zooms an area you have selected with -S,-E,-s,-e (all 4 are
optional).
- -z, --zoom-area [ [-S
<pos>] [-E <pos>] [-s <pos>] [-e <pos>]
]
- This option marks a zoom area on your plot, but does not make a zoom.
- -A, --alignment-name
<SeqXName:SeqYName>
- Defining which alignment is going to be plotted if you have more than one
alignment in your gff input.
- -N, --x-sequence-name
<SeqXName>
- Defining which sequence is going to be plotted at X-axis.
- -n, --y-sequence-name
<SeqYName>
- Defining which sequence is going to be plotted at Y-axis.
- -r,
--aplot-xy-noteq
- By default X and Y axes have same length, this option disables such
behaviour, so X and Y sequence will have axes-lengths proportional to
their nucleotide lengths.
- -R, --xy-axes-scale <X/Y
ratio>
- This option allows one to set a different scale between X and Y axes
lengths (by default is '1'). Below 1 values make Y larger than X, and
larger than 1 result in getting X larger than Y. # Must be explained
better.
- -W,
--aln-scale-width
- Scaling score on width for Aplot lines.
- -w,
--aln-scale-color
- Scaling score on color for Aplot lines.
- -K, --show-ribbons
<ribbon_type>
- Force Ribbons for all features on axes to be: (N)one, (L)ines, (R)ibbons,
(B)oth.
- -G, --show-grid
- Switches 'on' grid (default is 'off').
- -g, --hide-grid
- Switches 'off' grid (if switched on from customization files).
- -I,
--show-percent-box
- Switches 'on' Percent box (default is 'off').
- -i,
--hide-percent-box
- Switches 'off' Percent box (if set to 'on' on custom files).
- -O,
--show-extra-box
- Switches 'on' Extra box (default is 'off').
- -o,
--hide-extra-box
- Switches 'off' Extra box (if set to 'on' on custom files).
- -D, --aplot-box-color
<color>
- Aplot main box background color.
- -d, --percent-box-color
<color>
- Percent box background color.
- -b, --extra-box-color
<color>
- Extra box background color.
- --nopswarnings
- Switch off warnings that may appear on the final PostScript figure when X
sequence, Y sequence and/or alignment input data is missing.
- -a, --hide-credits
- Switch off gff2aplot credits line on plot.
- --debug
- Reporting variable contents when testing the program. Requires that log
report file option was also activated.
- --layout-var
'<variable=value>'
- --sequence-var
'<sequence::variable=value>'
- --source-var
'<source::variable=value>'
- --strand-var
'<strand::variable=value>'
- --group-var
'<group::variable=value>'
- --feature-var
'<feature::variable=value>'
- Loading a feature/group/strand/source/sequence/layout customization
variable from command-line. You can set several variables by repeating any
of these options, i.e.:
... --feature-var 'cds::feature_shape=box'
--feature-var 'cds::feature_color=blue' ...
- -C, --custom-filename
<filename>
- Loading customization parameters from a given file (if default
".gff2aplotrc" exists is loaded before it).
- Those are the colors defined
in gff2aplot:
-
+ Default Colors: black white.
+ Color Palette:
grey pink magenta violet blue skyblue cyan seagreen
green limegreen yellow orange red brown
You can get up to nine color shades from Variable Colors with
"verydeep", "deep", "verydark",
"dark", "light", "verylight",
"pale" and "verypale" prefixes, as example:
verydeepblue, deepblue, verydarkblue, darkblue, blue, lightblue,
verylightblue, paleblue and verypaleblue.
+ Dynamic colors: gradient rainbow.
The following page sizes are available: from A0 to A10, from
B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto,
statement and tabloid.
There are two environmental variables that can be set by users to
their preferences:
+ You can specify the path where gff2aplot can find the default files with
the shell variable "GFF2APLOT_CUSTOMPATH". Default value is the
path where you are running gff2aplot.
+ You can also define the default custom filename you will like with the
variable "GFF2APLOT_CUSTOMFILE", program default filename for
custom file is ".gff2aplotrc".
+ Now gff2aplot does not need to write any temporary file, so that previous
versions default temporary directory path variable
("GFF2APLOT_TMP") is no longer used.
+ Setting those vars in Bourne-shell and C-shell:
o Using a Bourne-Shell (e.g. bash):
export GFF2APLOT_CUSTOMPATH="path" export
GFF2APLOT_CUSTOMFILE="file_name"
o Using a C-Shell:
setenv GFF2APLOT_CUSTOMPATH "path" setenv GFF2APLOT_CUSTOMFILE
"file_name"
gff2aplot was written by Josep Francesc ABRIL FERRANDO
<jabril@imim.es>, Thomas WIEHE <twiehe@zedat.fu-berlin.de> and
Roderic GUIGO SERRA <rguigo@imim.es>.
This manual page was written by Nelson A. de Oliveira
<naoliv@gmail.com>, for the Debian project (but may be used by
others).