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isoSegmenter

A program for segmenting genomes into isochores

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License

isoSegmenter - A program for segmenting genomes into isochores

Copyright (C) 2013-2021 ITB - CNR

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Citation

If you use isoSegmenter in your work, please cite this manuscript:

Cozzi P, Milanesi L, Bernardi G. Segmenting the Human Genome into Isochores. Evolutionary Bioinformatics 2015;11:253-261. doi:10.4137/EBO.S27693

Requirements

isoSegmenter works on a Linux distribution with python 2.7 installed. Some python libraries are needed by isoSegmenter:

  • numpy
  • gdmodule
  • Pillow
  • matplotlib
  • biopython

You can install all those requirements by installing the appropriate Linux package for your distribution, or by using pip. More information on installation are available in INSTALL.md

Installation

isoSegmenter consist in a series of python scripts. You can install the software using git

$ git clone https://github.com/bunop/isoSegmenter.git

Then enter into isoSegmenter directory and install the package using pip (using python virtualenv is high recommeded). Note the final . after pip install. This will install packages inside current directory:

$ cd isoSegmenter
$ pip install .

To get more details on installation, please see INSTALL.md

Usage

isoSegmenter.py is the main application to execute isochores segmentation. It requires a single chromosome FASTA file as an input file (ONLY a chromosome inside a file). You can download genome sequences from UCSC, EnsEMBL or NCBI FTP sites. Output files can be .CSV data file (importable in Excel) and .png image file. For example, inside isoSegmenter/test directory there is the Human chromosome 21 (hg19) as a packed FASTA file. We can call isoSegmenter to draw an image and to get the segmentation .csv file. Enter inside isoSegmenter and type:

$ isoSegmenter.py --infile test/chr21.fa.gz --outfile chr21.isochores.csv --graphfile chr21.isochores.png --draw_legend

--infile: This is the FASTA input file. It could be plain/text or compressed with gzip/bz2
--outfile: This is the isochores .CSV output file
--graphfile: This is the isochores .PNG output file
--draw_legend: Draw a colored legend on the right side of the image

This will draw an image like this:

chr21.isochores

There are other options for manipulating graphs and segmentation, for instance you can change windows size or gap tolerance, if you need. You can get a brief description of them by running:

$ isoSegmenter.py --help

Others usage examples will be available (soon) on isoSegmenter Wiki