optimize_primers.py – Records base frequency for each position of a primer for optimization by modulating degeneracy.


Optimize primers takes an input primer hits file (created by analyze_primers.py) and generates an output file containing the base frequency for each position in the primer.

Only primer hits that exceed a given score threshold will be considered for the base frequency output.

Usage: optimize_primers.py [options]

Input Arguments:



-i, --hits_fp
Target primer hits file to generate base frequencies with.


-o, --output_dir
Specify output directory for linkers summary. [default: .]
-s, --score_type
Value to use from primer hits file to determine a given primer’s amplification success. Valid choices are weighted_score, overall_mismatches, tp_mismatches. Gibbs energy scores not currently implemented [default: weighted_score]
-t, --score_threshold
If primer has score at or below this parameter, the primer amplification is considered to be successful. [default: 2.0]


A tab-seperated text file will be generated containing the primer sequence, in 5’ to 3’ orientation, and the base frequencies for each nucleotide.

Standard Example usage:

optimize_primers.py [options] {-i hits_filepath [required]}

Use overall mismatches for scoring, set score threshold to only consider primer hits that are equal to or less than two mismatches:

optimize_primers.py -i primer2r_hits.txt -s overall_mismatches -t 2

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