https://github.com/mojaveazure/snptoseq

Capture contextual sequences for a SNP
https://github.com/mojaveazure/snptoseq

Last synced: 18 days ago
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Capture contextual sequences for a SNP

• Host: GitHub
• URL: https://github.com/mojaveazure/snptoseq
• Owner: mojaveazure
• Created: 2016-11-10T16:22:21.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-03-21T21:59:27.000Z (almost 8 years ago)
• Last Synced: 2024-10-15T09:11:17.263Z (2 months ago)
• Language: Python
• Size: 8.79 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# 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:

```bash

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](https://www.python.org/)

 - [BioPython](http://biopython.org/wiki/Biopython)

 - [overload](https://pypi.python.org/pypi/overload)

BioPython and overload are available through [PyPi](https://pypi.python.org/pypi) and can be downloaded using [pip3](https://pip.pypa.io/en/latest/installing/) (included with Python 3.4 or greater)