Tutorial

Installation

Requirements

  • Python 3

python modules

  • configparser
  • mysql-connector-python
pip install --allow-external mysql-connector-python mysql-connector-python
pip install configparser

In case you want to work using a virtual environment switch to that environment first (see Install Scythe in a virtual environment).

external software

Install emboss on debian-based systems:

sudo apt-get install emboss

Important: needleall from (the ubuntu package for) EMBOSS 6.6.0.0 causes problems. This program was tested and works with needleall from EMBOSS 6.4.0.0.

Install Scythe in a virtual environment

Install virtualenv via pip:

pip install virtualenv

Create a virtual environment that uses Python 3 and activate:

virtualenv -p /usr/bin/python3 python3env
source python3env/bin/activate

Finally, install the scythe package:

(python3env)you@host:~$ pip install scythe

Without virtual environment

Via pip:

pip install scythe

Using Scythe

There are three ways to use Scythe: GUI, command line parameters, or configuration file.

The GUI allows you to directy obtain data from ENSEMBL, have it converted and processed by Scythe.

If you are using local files, make sure you have directories prepared that contain the loc and fasta files, and that you have a grp file ready. (See Converters on how to convert other formats to loc or grp.)

Read more about configuration files under Configuration Files.

Graphical User Interface

Call the GUI via

scythe-gui.py

or with configuration file conf.py

scythe-gui.py conf.scy

Please note that Scythe will write intermediate files to the current working directory. You might want to create a new directory for each run beforehand. Data that was already downloaded from ENSEMBL will not be downloaded again. If you want to reuse this data but try different parameters, just change the output directory (via the GUI) and start Scythe from the same working directory.

Command Line Interface

Traceback (most recent call last):
  File "../../scythe/scythe.py", line 11, in <module>
    import configparser
ImportError: No module named configparser

Please note that you cannot automatically download sequences from ENSEMBL with scythe.py (see Downloading from ENSEMBL without the GUI).