Mercurial > repos > vimalkumarvelayudhan > riboplot

annotate README.rst @ 20:a013fc01d8f3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Merge
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Mon, 31 Aug 2015 14:42:53 +0100
parents cff63cf0dea8
children 60bbd8ebe314
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
1 ========
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
2 RiboPlot
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
3 ========
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
4
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
5 .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
6 :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
7
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
8 .. image:: https://img.shields.io/pypi/v/riboplot.svg
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
9 :target: https://pypi.python.org/pypi/riboplot
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
10
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
11
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
13
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
14 There are two programs in the package:
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
15
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
16 **riboplot**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
17
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
18 Plot and output read counts (csv) for a single transcript.
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
19
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
20 **ribocount**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
21
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
22 Output read counts for all transcripts in an alignment.
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
23
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
24 Free software: GPL license
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
25
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
26 Documentation: https://riboplot.readthedocs.org
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
27
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
28 Repository: https://github.com/vimalkumarvelayudhan/riboplot
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
29
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
30 Requirements
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
31 ------------
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
32 Python packages
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
33 ...............
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
34 * matplotlib ``1.3.1``
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
35 * pysam ``0.8.3``
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
36
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
37 If you have a virtualenv setup, these packages and their dependencies can be installed
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
38 using::
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
39
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
40 pip install matplotlib==1.3.1
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
41 pip install pysam==0.8.3
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
42
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
43 Bedtools
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
44 ........
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
45 RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed.
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
46
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
47 This release of riboplot has been tested with bedtools version ``2.17.0``.
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
48
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
49 On Ubuntu and derivatives, bedtools can be installed from the repositories using::
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
50
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
51 sudo apt-get install bedtools
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
52