https://github.com/audy/hdf5-dna

Examples and experiments of using HDF5 and h5py with biological sequence data
https://github.com/audy/hdf5-dna

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Examples and experiments of using HDF5 and h5py with biological sequence data

• Host: GitHub
• URL: https://github.com/audy/hdf5-dna
• Owner: audy
• Created: 2014-03-20T20:41:14.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-03-24T20:27:56.000Z (over 10 years ago)
• Last Synced: 2023-03-11T01:21:07.889Z (over 1 year ago)
• Language: Python
• Size: 301 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

        
# hdf5-dna

Examples and experiments of using HDF5 and h5py with biological sequence data.

## Features

- Create HDF5 database from any sequence format that BioPython supports

  (FASTA, FASTQ, ...)

- Quickly generate random samples of sequences

see `bin/*` for details.

## Help

```sh

for i in bin/*; do python $i --help; done

```

## Tests

Just run `test/test-hdf5-dna`.

### Pre-Commit Hook

Add this to `.git/hooks/pre-commit` to automatically run and check tests

after running `git commit`.

```sh

test/test-hdf5-dna 2>/dev/null

if [ $? -eq 0 ]; then

  echo "Tests passed."

else

  echo "Tests failed. Aborting commit."

  exit -1

fi

```

## Installation

`pip install -r requirements.txt`

## LICENSE

The MIT License (MIT)

Copyright (c) 2014 Austin G. Davis-Richardson

Permission is hereby granted, free of charge, to any person obtaining a

copy of this software and associated documentation files (the

"Software"), to deal in the Software without restriction, including

without limitation the rights to use, copy, modify, merge, publish,

distribute, sublicense, and/or sell copies of the Software, and to

permit persons to whom the Software is furnished to do so, subject to

the following conditions:

The above copyright notice and this permission notice shall be included

in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS

OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.

IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY

CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,

TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE

SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.