snp2fasta

Take list of SNPs and generate fasta files with flanks

Installation

git clone https://github.com/efriman/snp2fasta.git

cd snp2fasta

pip install .

Requires pysam, which in some cases may need to be installed separately using conda install -c bioconda pysam

Usage

snp2fasta input_table.txt --flank [INTEGER] --fasta reference_genome.fa --outname output [OPTIONS]

By default, character - is treated as deletion. Can be changed with --ignore_char

By default, both ends of ref and alt are trimmed for insertions so that the length does not exceed 2*flank. Can be changed by specifying --no_trim

Combinations of SNPs can be generated using --combinations k where k is the maximum number of combinations allowed (has to be at least 2). This will flank around the center of the SNPs within the maximum distance and generate up to k combinations of alleles in a separate file. Set maximum distance between SNPs using --maxdist.

Example inputs and output

snp2fasta input_table.txt --flank 5 --fasta reference_genome.fa --outname test --combinations 2 --maxdist 10

input_table.bed

chrom	start	ref	alt
chr1	6	A	G
chr2	11	C	T

test_matched.fa

>chr1_6_A

atgatAtagcc

>chr1_6_G

atgatGtagcc

>chr2_11_C

atagcCgtacg

>chr2_11_T

atagcTgtacg

test_combinations.fa

>chr1_6_A_chr1_11_C

atAtagcCgt

>chr1_6_G_chr1_11_C

atGtagcCgt

>chr1_6_A_chr1_11_T

atAtagcTgt

>chr1_6_G_chr1_11_T

atGtagcTgt