scythe 0.1a1

Find best matching set of transcripts for one-to-one orthologous genes from two or more species

Scythe, Selection of Conserved Transcript by Homology Evaluation, tries to find the best matching set of transcripts for each one-to-one orthologous gene from two or more species.

Usage (GUI):

scythe-gui.py

Usage (command line):

   ######################################
   # scythe.py v0.1a1                   #
   ######################################
 usage:
    scythe.py -i DIR -g .grpFILE -d DELIMITER --cleanup

 usage with configuration file:
    scythe.py --config configuration.scy

 general options:
   -C, --config                     use configuration file instead of
                                    command line parameters
   -c, --cleanup                    remove temporary files when done
   -h, --help                       prints this
   -i, --in_dir=DIR                 folder w/ subfolders "fa" and "loc"

   -o, --out_dir=DIR                output directory [default:./]
   -N, --num_cores=NUM              number of processors to use [default 1]

algorithm options:
   -R, --sl_ref                     find best matches to reference
   -G, --sl_glob                    best scoring pair as seed
   -M, --mx_sum                     optimize sum of pairwise scores


 alignment options:
    -O, --gap_open=FLOAT           needleall gap opening cost [default 10]
    -E, --gap_extend=FLOAT         needleall gap extension cost

 fasta options:
   -d, --delim=STRING               split fasta headers at STRING
   -a, --asID=INT                   use INTth part of fasta header as transcript-ID
                                    (default:0)

 further help:
   Please see documentation.

Installation

Scythe needs Python 3. You might want to set up a virtual environment with Python 3 for easier package management. Please see the documentation for more details. (In your virtual environment) install Scythe via

pip install scythe

Requirements

Python modules

• configparser

• mysql-connector-python

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

External programs

• needleall (version 6.3.1; EMBOSS package, http://emboss.sourceforge.net/)