Mercurial > repos > davidmurphy > codonlogo

annotate README.txt @ 13:cd6c4bd14718

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidmurphy
date Fri, 24 Feb 2012 09:26:11 -0500
parents f3462128e87c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
1
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
3 logos from biological sequence alignments. It can be run on the command line,
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
4 as a standalone webserver or as a CGI webapp.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
5
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
6
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
7 For help on the command line interface run
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
8 ./codonlogo --help
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
10 To build a simple logo run
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
11 ./codonlogo < cap.fa > logo.eps
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
12
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
13
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
14 To run as a standalone webserver at localhost:8080
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
15 ./codonlogo --server
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
16
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
17
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
18 An example file of probabilities is included, examplepriorfile.txt
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
19 It can be used with the following command.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
20
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
22
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
23
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
24 examplepriorfile contains the frequencies for codons in human CDS regions.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
25
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
26
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
27 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
28 This is not believed to be a problem with CodonLogo.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
29 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
30
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
31 For converting files to a suitable format the following sites can be used:
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
32
8
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
33 http://genome.nci.nih.gov/tools/reformat.html
5149eb3a89c2 Uploaded
davidmurphy
parents: 4
diff changeset
34 http://www-bimas.cit.nih.gov/molbio/readseq/
9
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
35
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
36
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
37
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
38
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
39 -- Distribution and Modification --
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
40 This package is distributed under the new BSD Open Source License.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
41 Please see the LICENSE.txt file for details on copyright and licensing.
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
42 The CodonLogo source code can be downloaded from
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
43 http://recode.ucc.ie/CodonLogo
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
44
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
45 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
46 computational biology (http://code.google.com/p/corebio), and the python
f3462128e87c Minor alterations to the galaxy interface with some better examples and error messages added.
davidmurphy
parents: 8
diff changeset
47 array package 'numpy' (http://www.scipy.org/Download)