SNPtoSEQ.py is a simple Python program that captures SNP contextual sequence and provides a BED and/or FASTA file with the sequences
$ ./SNPtoSEQ.py
usage: SNPtoSEQ.py -v VCF FILE -r REFERENCE FASTA FILE [-w WINDOW SIZE]
[-o OUTPUT NAME] [--no-fasta | --no-bed]
Capture SNP contextual sequences into BED and/or FASTA format
Input Options:
Provide a VCF file of SNPs and a reference genome in FASTA format
-v VCF FILE, --vcf VCF FILE
SNPs in VCF format
-r REFERENCE FASTA FILE, --reference REFERENCE FASTA FILE
Reference genome in FASTA format
Window options:
Select a one-sided window size to capture in contextual sequence; this
size represents the amount of sequence on each side of the SNP to capture
-w WINDOW SIZE, --window WINDOW SIZE
Set the window size, defaults to 120
Output Options:
Provide an output name as well as choose if we suppress some output
-o OUTPUT NAME, --outname OUTPUT NAME
Basename for the output file(s), defaults to the name
of '-v | --vcf' with modified extensions
--no-fasta Do we suppress FASTA output? Incompatible with '--no-
bed'
--no-bed Do we suppress BED output? Incompatible with '--no-
fasta'
SNPtoSEQ.py requires a VCF file with SNP information and a reference genome in FASTA format. Please ensure that the chromosome information in the VCF matches the sequence identifiers in the FASTA file. To check, use UNIX grep and cut to find the chromosome information in both files:
grep -v '#' ${MY_VCF} | cut -f 1
grep '>' ${MY_REFERENCE}SNPtoSEQ.py creates between one and two output files:
| File name | Contents |
|---|---|
| output.bed | BED file describing the SNP contextual sequence; suppressed with --no-bed |
| output.fasta | FASTA file with containing the SNP contextual sequences; sequence identifiers are the SNP name; suppressed-with --no-fasta |
SNPtoSEQ.py depends on the following:
BioPython and overload are available through PyPi and can be downloaded using pip3 (included with Python 3.4 or greater)