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