https://github.com/audy/nearproteins

:mag: :book: Amino Acids Database with Fuzzy Querying
https://github.com/audy/nearproteins

Last synced: about 21 hours ago
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:mag: :book: Amino Acids Database with Fuzzy Querying

• Host: GitHub
• URL: https://github.com/audy/nearproteins
• Owner: audy
• License: mit
• Created: 2014-09-29T16:28:22.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2016-07-26T19:57:35.000Z (about 8 years ago)
• Last Synced: 2023-03-11T01:21:34.811Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 2.6 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: readme.md
  • License: LICENSE

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README

        
# nearproteins

Store for finding similar amino acid sequences using Locality Sensitive Hashing

and Approximate Nearest Neighbors.

## Installation

Python, with dependencies:

- Annoy

- BioPython

```

pip install -r requirements.txt

```

Redis

## Instructions

1. Load proteins into database

```sh

$ ./load-proteins < data/proteins.fasta

```

2. Query database

```sh

$ ./query-proteins < data/proteins.fasta # returns JSON for each record

```

## Python API

Very basic. I plan to add more configuration.

### Loading data into store

```python

from Bio import SeqIO

import nearproteins

store = nearproteins.SimilarStringStore()

store.engine.clean_all_buckets()

records = SeqIO.parse(handle, 'fasta')

for record in records:

    store.add(str(record.seq), record.id)

```

### Retrieving records from store

```python

# returns array of vectors, match IDs, similarities

results = store.get(str(record.seq)) 

```

## Use as a server

You can query and add records to the database using simple sockets.

```sh

$ ./server # start the server, listens on port 1234

```

In another window...

```sh

$ nc 127.0.0.1 1234 # connect

SET 1 AUSTIN

SET 2 BOSTON

GET AUSTIN

{"1": 0.0}

GET BOSTON

{"2": 0.0}

```

You can use this to build a simple client in another language such as Ruby

```ruby

require 'dna'

require 'socket'

require 'json'

HOSTNAME = '127.0.0.1'

PORT = '1234'

socket = TCPSocket.open HOSTNAME, PORT

File.open('proteins.fasta') do |handle|

  records = Dna.new handle, :format => :fasta

  records.each do |record|

    socket.puts "GET #{record.sequence}"

    resp = JSON.parse(socket.gets)

    p resp

  end

end

```