Mercurial > repos > davidmurphy > codonlogo
comparison README.txt @ 4:4d47ab2b7bcc
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| author | davidmurphy |
|---|---|
| date | Fri, 13 Jan 2012 07:18:19 -0500 |
| parents | |
| children | 5149eb3a89c2 |
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| 1 | |
| 2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence | |
| 3 logos from biological sequence alignments. It can be run on the command line, | |
| 4 as a standalone webserver or as a CGI webapp. | |
| 5 | |
| 6 | |
| 7 For help on the command line interface run | |
| 8 ./codonlogo --help | |
| 9 | |
| 10 To build a simple logo run | |
| 11 ./codonlogo < cap.fa > logo.eps | |
| 12 | |
| 13 | |
| 14 To run as a standalone webserver at localhost:8080 | |
| 15 ./codonlogo --server | |
| 16 | |
| 17 | |
| 18 An example file of probabilities is included, examplepriorfile.txt | |
| 19 It can be used with the following command. | |
| 20 | |
| 21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps | |
| 22 | |
| 23 | |
| 24 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. | |
| 25 This is not believed to be a problem with CodonLogo. | |
| 26 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript. | |
| 27 | |
| 28 | |
| 29 | |
| 30 -- Distribution and Modification -- | |
| 31 This package is distributed under the new BSD Open Source License. | |
| 32 Please see the LICENSE.txt file for details on copyright and licensing. | |
| 33 The CodonLogo source code can be downloaded from | |
| 34 http://recode.ucc.ie/CodonLogo | |
| 35 | |
| 36 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for | |
| 37 computational biology (http://code.google.com/p/corebio), and the python | |
| 38 array package 'numpy' (http://www.scipy.org/Download) |