An easy-to-use Python API for Primer3 primer design.
Project description
Primer3Plus
Primer3Plus is a Python DNA primer design tool based off of Primer3 and the Python primer3 wrapper (https://pypi.org/project/primer3-py/).
import json design = Design() template = """ TCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCAC ATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAG GTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTAT TTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGC ATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGC TCGAAGGCTTTAATTTGC """ template = template.replace('\n', '').replace(' ', '') design.settings.template(template) design.settings.as_cloning_task() design.settings.primer_num_return(1) results, explain = design.run() print(json.dumps(results, indent=1)) print(json.dumps(explain, indent=1))
{ "0": { "PAIR": { "PENALTY": 11.204301707622733, "COMPL_ANY_TH": 0.0, "COMPL_END_TH": 0.0, "PRODUCT_SIZE": 248 }, "LEFT": { "PENALTY": 9.027129166714644, "SEQUENCE": "TCATGTAATTAGTTATGTCACGCTTAC", "location": [ 0, 27 ], "TM": 57.972870833285356, "GC_PERCENT": 33.333333333333336, "SELF_ANY_TH": 0.0, "SELF_END_TH": 0.0, "HAIRPIN_TH": 0.0, "END_STABILITY": 2.34 }, "RIGHT": { "PENALTY": 2.1771725409080886, "SEQUENCE": "GCAAATTAAAGCCTTCGAGCG", "location": [ 247, 21 ], "TM": 58.82282745909191, "GC_PERCENT": 47.61904761904762, "SELF_ANY_TH": 0.0, "SELF_END_TH": 0.0, "HAIRPIN_TH": 38.006257959698985, "END_STABILITY": 5.03 } } } { "PRIMER_LEFT_EXPLAIN": "considered 10, low tm 9, ok 1", "PRIMER_RIGHT_EXPLAIN": "considered 10, low tm 3, high tm 4, ok 3", "PRIMER_PAIR_EXPLAIN": "considered 1, ok 1", "PRIMER_LEFT_NUM_RETURNED": 1, "PRIMER_RIGHT_NUM_RETURNED": 1, "PRIMER_INTERNAL_NUM_RETURNED": 0, "PRIMER_PAIR_NUM_RETURNED": 1 }
Installation
pip install primer3plus -U
Requirements
python >= 3.5
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