Take list of SNPs and generate fasta files with flanks
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
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.
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