https://github.com/ciaranomara/stamp.jl

Load GEM's default PFM output
https://github.com/ciaranomara/stamp.jl

bioinformatics julia pfm stamp

Last synced: about 1 year ago
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Load GEM's default PFM output

• Host: GitHub
• URL: https://github.com/ciaranomara/stamp.jl
• Owner: CiaranOMara
• License: mit
• Created: 2019-06-06T04:20:15.000Z (about 7 years ago)
• Default Branch: develop
• Last Pushed: 2020-05-15T13:10:46.000Z (about 6 years ago)
• Last Synced: 2024-10-19T15:20:06.471Z (over 1 year ago)
• Topics: bioinformatics, julia, pfm, stamp
• Language: Julia
• Homepage:
• Size: 9.77 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# STAMP.jl

[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)

[![Latest Release](https://img.shields.io/github/release/CiaranOMara/STAMP.jl.svg)](https://github.com/CiaranOMara/STAMP.jl/releases/latest)

[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/CiaranOMara/STAMP.jl/blob/master/LICENSE)

[![Unit tests](https://github.com/CiaranOMara/STAMP.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/CiaranOMara/STAMP.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)

[![codecov](https://codecov.io/gh/CiaranOMara/STAMP.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/CiaranOMara/STAMP.jl)

> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/ "original blog post").

## Description

Initially written to load [GEM](http://groups.csail.mit.edu/cgs/gem/)'s default PFM output.

Inspired by [FASTX.jl](https://github.com/BioJulia/FASTX.jl).

## Installation

Install STAMP from the Julia REPL:

```julia

] clone https://github.com/CiaranOMara/STAMP.jl

```

## Usage

### Read records

```julia

using STAMP

reader = open(STAMP.Reader, file)

record = read(reader) #TODO: read all records.

```

```julia

using STAMP

reader = open(STAMP.Reader, file)

for record in reader

    # Do something

end

close(reader)

```

```julia

using STAMP

reader = open(STAMP.Reader, file)

record = STAMP.Record()

read!(reader, record))

# Do something

close(reader)

```

```julia

using STAMP

open(STAMP.Reader, file) do reader

    for record in reader

        # Do something

    end

end

```