snprimer 0.2.0

Small python library to search snp in primer by position or by sequence.

SNPrimer

Small python library to search snp in primer by position or by sequence.

Installation

pip install snprimer

Usage

🎯 By position 🎯

from snprimer import PositionRange

position = PositionRange("chr8",19818430, 19818440)
print(position)
# PositionRange(chr='chr8', start=19818430, end=19818440, strand=None, snp=[SNP(id='chr8:g.19818436C>G', rsid='rs316', vaf=0.15300000000000002), SNP(id='chr8:g.19818436C>T', rsid='rs316', vaf=0.15300000000000002)])
for snp in position.get_snp(max_vaf=0.05):
    print(snp)
#SNP(id='chr8:g.19818436C>G', rsid='rs316', vaf=0.15300000000000002)
#SNP(id='chr8:g.19818436C>T', rsid='rs316', vaf=0.15300000000000002)

🔤 By sequence 🔤

from snprimer import Primer

primer = Primer("CACACAGATCAGAGGGCCAAC")
print(primer)
#Primer(seq='CACACAGATCAGAGGGCCAAC', position_ranges=[PositionRange(chr='chr1', start=26774827, end=26774847, strand='+', snp=[SNP(id='chr1:g.26774827G>A', rsid='rs2075289787', vaf=0), SNP(id='chr1:g.26774830A>G', rsid='rs986550282', vaf=0.0), SNP(id='chr1:g.26774842T>C', rsid='rs1440652363', vaf=0.0)])])
primer.infos(max_vaf=0)
#CACACAGATCAGAGGGCCAAC has snp with vaf > 0 : [SNP(id='chr1:g.26774827G>A', rsid='rs2075289787', vaf=0), SNP(id='chr1:g.26774830A>G', rsid='rs986550282', vaf=0.0), SNP(id='chr1:g.26774842T>C', rsid='rs1440652363', vaf=0.0)]

🖥️In silico PCR🖥️

from pathlib import Path
from snprimer import Primer, PrimerPair

a = Primer("GGAGATGTACAGCGTGCCATAC", "hg19")
b = Primer("TACATCTTGCTGAGGGGAAGGC", "hg19")
pp = PrimerPair(a, b)
pcr = pp.make_pcr(Path('/path/to/hg19.fa'))
print(pcr)