Working on swissprot.

- **wget**

- **gzip**

## RAM requirements

To be measured.

## Steps

**It downloads the current version of the data.**

Execute to download all necessary files.

Execute the following to download and prepare the dataset.

```bash

./download_prepare.sh

```

Execute to convert the raw data file into bracket notation. **Takes some time.**

```bash

python swissprot_to_bracket.py

```

Execute to sort the dataset by tree size.

```bash

./sort_dataset.sh swissprot.bracket

```

## Estimated time

To be measured.

#!/bin/bash

# file: prepare_data.sh

# The MIT License (MIT)

# Copyright (c) 2017 Thomas Hütter, Mateusz Pawlik.

# 

# Program: Downloads and prepares data containing the swissprot dataset.

# 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:

# 

# Author: Thomas Huetter

# create target folder and change into it

mkdir data

cd data

# 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.

# download the data files

# Download the data files.

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz

# gunzip the data to uniprot_sprot.xml

# Extract the dataset.

gunzip uniprot_sprot.xml.gz

# remove gzip file

rm -rf uniprot_sprot.xml.gz 

# Convert XML to bracket notation.

./swissprot_to_bracket.py

# next steps can be seen in README.md

# convert file to bracket notation

# Sort the dataset.

./../utilities/sort_dataset.sh swissprot.bracket > swissprot_sorted.bracket

# select random line with random_lines.py and sort them with sort_dataset.sh

 No newline at end of file

# Tidy up.

rm *xml*

rm swissprot.bracket

#!/usr/bin/env python3

# The MIT License (MIT)

# Copyright (c) 2017 Thomas Hütter, Mateusz Pawlik.

# 

# 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.

from lxml import etree

import lxml.sax

from xml.sax.handler import ContentHandler

# This script converts DBLP from XML to bracket notation.

# NOTE: Filenames are hardcoded in this script.

# This class implements the sax-like events for converting XML elemnts into

# bracket-notation nodes and labels.

class SwissprotContentHandler(ContentHandler):

    swissprot_bracket.write(handler.bn + "\n")

print("--- Closing output files.")

swissprot_bracket.close()

 No newline at end of file