Preprocessing

Installation

Several files need to be preprocessed in order to use the BLS speller. The orthologous families can be created with the prepInput tool like this:

1# clone git repo if not done yet
2git clone https://dries_decap@bitbucket.org/dries_decap/suffixtree-motif-speller.git
3cd suffixtree-motif-speller/process_input
4mkdir build
5cd build
6cmake ../
7make

Execution

This tool requires three inputs:

  • an orthology file: a tab separated file with this format per line #ID\tNumGenes\tNumSpecies\tspace separated gene list

  • a folder with a subfolder per species (by name) with a fasta file in that species folder where there is a promotor sequence available for all the genes present in the orthology file.

  • a newick tree that represents the present species

And can be run like this:

1./prepInput ${fasta_files_folder} ${orthology_file} ${newick_tree_file} ${outputfolder}