mojaveazure / snptoseq

Capture contextual sequences for a SNP

SNPtoSEQ.py

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'

Inputs

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}

Outputs

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

Dependencies

SNPtoSEQ.py depends on the following:

• Python 3
• BioPython
• overload

BioPython and overload are available through PyPi and can be downloaded using pip3 (included with Python 3.4 or greater)