# FastaRead
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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](http://genomewiki.ucsc.edu/index.php/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

1. Fork it ( http://github.com/sfcarroll/ruby-fasta-read/fork )
2. Create your feature branch (`git checkout -b my-new-feature`)
3. Commit your changes (`git commit -am 'Add some feature'`)
4. Push to the branch (`git push origin my-new-feature`)
5. Create new Pull Request