Working on swissprot.

swissprot/README.md

@@ -25,25 +25,19 @@ https://www.uniprot.org/downloads
 - **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.

swissprot/download_prepare.sh

 #!/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

swissprot/swissprot_to_bracket.py

+#!/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):
@@ -53,3 +80,4 @@ for child in root:
     swissprot_bracket.write(handler.bn + "\n")
 
 print("--- Closing output files.")
+swissprot_bracket.close()
\ No newline at end of file