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pvhelden / optimize-matrix-GA

Optimise one or several position-specific scoring matrices based on their capability to discriminate positive from negative sequence sets.
GNU Affero General Public License v3.0
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optimize-matrix-GA

Optimize position specific scoring matrices (PSSM) according to their capability to discriminate a positive from a negative sequence set.

Requirements

A local instance of the software suite Regulatory Sequence Analysis Tools (RSAT).

See INSTALL.md for the instlalation instructions.

Usage example

The local python installation should contain all the required libraries.

export PYTHON_PATH=venv/Downloads/bin/python # python path should be adapted to your local settings
$PYTHON_PATH optimize-matrix-GA.py -v 3 -t 10 -g 5 -c 5 -s 5 \
  -m data/matrices/PRDM5_GHTS_YWK_B_AffSeq_B1_PRDM5.C2_peakmo-clust-trimmed.tf \
  -p data/sequences/YWK_B_AffSeq_B1_PRDM5.C2.fasta \
  -n data/sequences/YWK_B_AffSeq_B1_PRDM5.C2_rand-loci.fa \
  -b data/bg_models/equiprobable_1str.tsv \
  -r "${RSAT_CMD}" \
  -o results/optimized_matrices/PRDM5_GHTS_YWK_B_AffSeq_B1_PRDM5.C2_peakmo-clust-trimmed/PRDM5_GHTS_YWK_B_AffSeq_B1_PRDM5.C2_peakmo-clust-trimmed_