Provided by: python3-weblogo_3.8.0-2_all 
NAME
WebLogo - create sequence logos from biological sequence alignments
SYNOPSIS
weblogo [options] < sequence_data.fa > sequence_logo.eps
DESCRIPTION
Create sequence logos from biological sequence alignments.
OPTIONS
--version
show program's version number and exit
-h --help
show this help message and exit
Input/Output Options:
-f --fin FILENAME
Sequence input file (default: stdin)
--upload URL
Upload input file from URL
-D --datatype FORMAT
Type of multiple sequence alignment or position weight matrix file: (clustal,
fasta, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array,
transfac)
-o --fout FILENAME
Output file (default: stdout)
-F --format FORMAT
Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata, csv
Logo Data Options:
-A --sequence-type TYPE
The type of sequence data: 'protein', 'rna' or 'dna'.
-a --alphabet ALPHABET
The set of symbols to count, e.g. 'AGTC'. All characters not in the alphabet are
ignored. If neither the alphabet nor sequence-type are specified then weblogo will
examine the input data and make an educated guess. See also --sequence-type,
--ignore-lower-case
-U --units UNIT
A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit offree energy
('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities
--composition COMP.
The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none'
(do not perform any compositional adjustment), a CG percentage, a species name
(e.g. 'E. coli', 'H. sapiens'), or an explicit distribution (e.g. "{'A':10, 'C':40,
'G':40, 'T':10}"). The automatic option uses a typical distribution for proteins
and equiprobable distribution for everything else.
--weight NUMBER
The weight of prior data. Default depends on alphabet length
-i --first-index INDEX
Index of first position in sequence data (default: 1)
-l --lower INDEX
Lower bound of sequence to display
-u --upper INDEX
Upper bound of sequence to display
Transformations:
Optional transformations of the sequence data.
--ignore-lower-case
Disregard lower case letters and only count upper case letters in sequences.
--reverse
reverse sequences
--complement
complement nucleic sequences
--revcomp
reverse complement nucleic sequences
Logo Format Options:
These options control the format and display of the logo.
-s --size LOGOSIZE
Specify a standard logo size (small, medium (default), large)
-n --stacks-per-line COUNT
Maximum number of logo stacks per logo line. (default: 40)
-t --title TEXT
Logo title text.
--label TEXT
A figure label, e.g. '2a'
-X --show-xaxis YES/NO
Display sequence numbers along x-axis? (default: True)
-x --xlabel TEXT
X-axis label
--annotate TEXT
A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'. Annotation
list must be same length as sequences.
--rotate-numbers YES/NO
Draw X-axis numbers with vertical orientation (default: False).
--number-interval NUMBER
Distance between numbers on X-axis (default: 5)
-S --yaxis NUMBER
Height of yaxis in units. (Default: Maximum value with uninformative prior.)
-Y --show-yaxis YES/NO
Display entropy scale along y-axis? (default: True)
-y --ylabel TEXT
Y-axis label (default depends on plot type and units)
-E --show-ends YES/NO
Label the ends of the sequence? (default: False)
-P --fineprint TEXT
The fine print (default: weblogo version)
--ticmarks NUMBER
Distance between ticmarks (default: 1.0)
--errorbars YES/NO
Display error bars? (default: True)
--reverse-stacks YES/NO
Draw stacks with largest letters on top? (default: True)
Color Options:
Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc
-c --color-scheme SCHEME
Specify a standard color scheme (auto, base pairing, charge, chemistry, classic,
hydrophobicity, monochrome)
-C --color COLOR SYMBOLS DESCRIPTION
Specify symbol colors, e.g. --color black AG 'Purine' --color red TC 'Pyrimidine'
--default-color COLOR
Symbol color if not otherwise specified.
Font Format Options:
These options provide control over the font sizes and types.
--fontsize POINTS
Regular text font size in points (default: 10)
--title-fontsize POINTS
Title text font size in points (default: 12)
--small-fontsize POINTS
Small text font size in points (default: 6)
--number-fontsize POINTS
Axis numbers font size in points (default: 8)
--text-font FONT
Specify font for labels (default: ArialMT)
--logo-font FONT
Specify font for logo (default: Arial-BoldMT)
--title-font FONT
Specify font for title (default: ArialMT)
Advanced Format Options:
These options provide fine control over the display of the logo.
-W --stack-width POINTS
Width of a logo stack (default: 10.8)
--aspect-ratio POINTS
Ratio of stack height to width (default: 5)
--box YES/NO
Draw boxes around symbols? (default: no)
--resolution DPI
Bitmap resolution in dots per inch (DPI). (Default: 96 DPI, except png_print, 600
DPI) Low resolution bitmaps (DPI<300) are antialiased.
--scale-width YES/NO
Scale the visible stack width by the fraction of symbols in the column? (I.e.
columns with many gaps of unknowns are narrow.) (Default: yes)
--debug YES/NO
Output additional diagnostic information. (Default: False)
--errorbar-fraction NUMBER
Sets error bars display proportion (default: 0.9)
--errorbar-width-fraction NUMBER
Sets error bars width display proportion (default: 0.25)
--errorbar-gray NUMBER
Sets error bars' gray scale percentage (default: 0.75)
WebLogo Server:
Run a standalone webserver on a local port.
--serve
Start a standalone WebLogo server for creating sequence logos.
--port PORT
Listen to this local port. (Default: 8080)