Small python library to search snp in primer by position or by sequence.
pip install snprimer
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)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)])])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)from snprimer import PrimerMaker, PositionRange
from pathlib import Path
seq_args = {
}
global_args = {
"PRIMER_EXPLAIN_FLAG": 1,
"PRIMER_MAX_END_STABILITY": 9.0,
"PRIMER_MAX_LIBRARY_MISPRIMING": 18.00,
"PRIMER_PAIR_MAX_LIBRARY_MISPRIMING": 50.00,
"PRIMER_MIN_SIZE": 17,
"PRIMER_OPT_SIZE": 22,
"PRIMER_MAX_SIZE": 27,
"PRIMER_MIN_TM": 58,
"PRIMER_OPT_TM": 61,
"PRIMER_MAX_TM": 63,
"PRIMER_MAX_DIFF_TM": 100,
"PRIMER_MIN_GC": 20,
"PRIMER_MAX_GC": 80,
"PRIMER_SELF_END": 9.00,
"PRIMER_MAX_POLY_X": 5,
"PRIMER_GC_CLAMP": 0,
"PRIMER_PRODUCT_SIZE_RANGE": [[70, 160]],
}
position_range = PositionRange("chr1",27100919,27100919)
ref_fasta = Path("/path/to/fasta")
print(PrimerMaker(ref_fasta,
seq_args, global_args).get_primers(position_range)[0]
.make_pcr(ref_fasta))
#[>chr1:27100876-27100999
#GGAGATGTACAGCGTGCCATACAGCACTGGGCAGGGGCAGCCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCCCCAGCCTGCCAGCCAGCAACAAGCTGCCCAGCCTTCCCCTCAGCAAGATGTA]You can also use SNPrimer in cli with two options :
- check will check the presence of snp in a position range
- pcr will make the insilico pcr
git clone [email protected]:Benoitdw/SNPrimer.git
cd SNPrimer
python -m venv venv # recommended work in a virtual environment
source venv/bin/activate # Recommended activate the virtual environment
poetry install
# OR pip install .Usage: main.py check [OPTIONS] POSITION_FILE [OUTPUT]
Options:
--vaf FLOAT minimum snp vaf to reportpython main.py check --vaf 0.00 tests/files/position.tsv tests/files/output_position.tsv
will produce the output_position.tsv file you can see in tests/files directory
[] Remake cli [] Custom blast [] cross primer hybridization [] Better unit tests
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