=================
Quickstart Guide
=================
Installation and configuration
==============================
1. To install Segway first install `Genomedata
`_
and `GMTK
`_, then run this command
from :program:`bash`::
pip install segway
2. If you are using SGE, your system administrator must set up a
``mem_requested`` resource for Segway to work. This can be done by
installing Segway and then running ``python -m
segway.cluster.sge_setup``.
Acquiring data
==============
3. Observation data is stored with the genomedata system.
. There is a small
Genomedata archive for testing that comes with Segway, that is used
in the below steps. You can get it using::
wget http://pmgenomics.ca/hoffmanlab/proj/segway/2011/test.genomedata
Running Segway
==============
4. Use the ``segway train`` command to discover patterns in the test
data. Here, we specify that we want Segway to discover four unique
patterns::
segway --num-labels=4 train test.genomedata traindir
5. Use the ``segway identify`` command to create the segmentation,
which partitions the genome into regions labeled with one of the
four discovered patterns::
segway identify test.genomedata traindir identifydir
.. note::
This example spawns jobs that will run sequentially due to small
segment size. See the :option:`--split-sequences` option for
dividing segments into smaller pieces.
Results
=======
6. The ``identifydir/segway.bed.gz`` file has each segment as a
separate line in the BED file, and can be used for further
processing.
7. The ``identifydir/segway.layered.bed.gz`` file is designed for
easier visualization on a genome browser. It has thick lines where
a segment is present and thin lines where it is not. This is not as
easy for a computer to parse, but it is more useful visually.
8. You can also perform further analysis of the segmentation and
trained parameters using Segtools
.