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

Description:

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:

Note

[REQUIRED]

-i, --hits_fp

Target primer hits file to generate base frequencies with.

[OPTIONAL]

-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]

Output:

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