 |
 |
 |
This page was last updated on Friday, 08-Apr-2016 13:54:17 CDT
Version 3.x link https://github.com/WebLogo/weblogo
WebLogo 2.x requires a recent version of gs (ghostscript) <http://www.cs.wisc.edu/~ghost/> to create PNG and PDF output, and ImageMagic's convert <http://www.imagemagick.org/> to create GIFs.
Downloading/unpacking weblogo Running setup.py egg_info for package weblogo Installing collected packages: weblogo Running setup.py install for weblogo changing mode of /usr/local/bin/transformseq to 775 changing mode of /usr/local/bin/weblogo to 775 Successfully installed weblogo Cleaning up...
Usage: weblogo [options] < sequence_data.fa > sequence_logo.eps 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) -D --datatype FORMAT Type of multiple sequence alignment or position weight matrix file: (clustal, fasta, plain, 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 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 NUMBER A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free 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. -S --yaxis UNIT 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. 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) 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)