BioFastaRead
A Ruby command-line program that will take coordinates and return either a unmasked gene sequence or a snp-masked sequence. The coordinates refer to the start and stop positions, and are "UCSC coordinates" i.e. 0 based and half open (see UCSC_coordinate_transforms)
Compatibility
Ruby versions:
- MRI 1.9.3
- MRI 2.0
- MRI 2.1
Installation
Add this line to your application's Gemfile:
gem 'fasta_read'
And then execute:
$ bundle
Or install it yourself as:
$ gem install fasta_read
Usage
fasta_read [options] assembly chromosome cstart cend
Example
fasta_read hg19 chr12 112123514 112123790 --output=out.txt
Options:
-h, --help Show command line help
-o, --output OUTPUTFILE outputs sequence to a file
--snp return the sequence from the SNP-masked assembly
--version Show help/version info
--log-level LEVEL Set the logging level
(debug|info|warn|error|fatal)
(Default: info)
Arguments
assembly
assembly name (hg19, mm10, etc.)
chromosome
id of chromosome (chr1-chr22 or chrx/chry)
cstart
start coordinate (inclusive) within the chromosome
cend
end coordinate within the chromosome
Program output
stdout: Extracted sequence (only)
stderr: Any errors.
using --output option exports the sequence to a file
Supporting Requirements
The program depends on being run at the top of a directory tree containing .fa files. The .fa files should be of the form where each file maps to a single chomosome. The directory tree will have separate branches for SNPs and unmasked files.
For example, provided the following tree the command expects to be run inside the 'fasta' directory:
fasta
├── hg19
│ ├── snp
│ │ ├── chr1.subst.fa
| │ ├── chr2.subst.fa
| │ ├── chr3.subst.fa
| │ └── ....
│ └── unmasked
│ ├── chr1.fa
| ├── chr2.fa
| ├── chr3.fa
| └── ....
└── mm10
├── snp
│ ├── chr1.subst.fa
│ ├── chr2.subst.fa
│ ├── chr3.subst.fa
│ └── ....
└── unmasked
├── chr1.fa
├── chr2.fa
├── chr3.fa
└── ....
Fasta files can be downloaded at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp138Mask/
Contributing
- Fork it ( http://github.com/sfcarroll/ruby-fasta-read/fork )
- Create your feature branch (
git checkout -b my-new-feature) - Commit your changes (
git commit -am 'Add some feature') - Push to the branch (
git push origin my-new-feature) - Create new Pull Request