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WebLogo (http://code.google.com/p/weblogo/) is a tool for creating sequence
logos from biological sequence alignments. It can be run on the command line,
as a standalone webserver, as a CGI webapp, or as a python library.
The main WebLogo webserver is located at http://weblogo.threeplusone.com
Please consult the manual for installation instructions and more information:
(Also located in the weblogolib/htdocs subdirectory.)
http://weblogo.threeplusone.com/manual.html
For help on the command line interface run
./weblogo --help
To build a simple logo run
./weblogo < cap.fa > logo0.eps
To run as a standalone webserver at localhost:8080
./weblogo --serve
To create a logo in python code:
>>> from weblogolib import *
>>> fin = open('cap.fa')
>>> seqs = read_seq_data(fin)
>>> data = LogoData.from_seqs(seqs)
>>> options = LogoOptions()
>>> options.title = "A Logo Title"
>>> format = LogoFormat(data, options)
>>> fout = open('cap.eps', 'w')
>>> eps_formatter( data, format, fout)
-- Distribution and Modification --
This package is distributed under the new BSD Open Source License.
Please see the LICENSE.txt file for details on copyright and licensing.
The WebLogo source code can be downloaded from
http://code.google.com/p/weblogo/
WebLogo requires Python 2.5, 2.6 or 2.7, and the python
array package 'numpy' (http://www.scipy.org/Download)
Generating logos in PDF or bitmap graphics formats require that the ghostscript
program 'gs' be installed. Scalable Vector Graphics (SVG) format also requires
the program 'pdf2svg'.
Version: 3.2
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GhostscriptAPI Interface to the command line program Ghostscript ('gs') |
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LogoOptions A container for all logo formatting options. |
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LogoFormat Specifies the format of the logo. |
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LogoData The data needed to generate a sequence logo. |
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| Variables | |
description = "Create sequence logos from biological sequence
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classic = ColorScheme([ColorGroup("G", "orange"), ColorGroup("
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std_color_schemes = {"auto": None, "monochrome": monochrome, "
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default_color_schemes = {unambiguous_protein_alphabet: hydroph
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std_units = {"bits": 1./ log(2), "nats": 1., "digits": 1./ log
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std_sizes = {"small": 5.4, "medium": 5.4* 2, "large": 5.4* 3}
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std_alphabets = {'protein': unambiguous_protein_alphabet, 'rna
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std_percentCG = {'H. sapiens': 40., 'E. coli': 50.5, 'S. cerev
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formatters = {'eps': eps_formatter, 'pdf': pdf_formatter, 'png
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| Function Details |
Read sequence data from the input stream and return a seqs object. The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument. Used to limit the load on the WebLogo webserver. |
| Variables Details |
description
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classic
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std_color_schemes
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default_color_schemes
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std_units
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std_alphabets
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std_percentCG
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formatters
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