XML Parser for LRG files

An XML parser in Python for producing a .bed file from an LRG_xml file obtained from the LRG-Sequence website "https://www.lrg-sequence.org".

n.b. This program is designed at this time to only work with the GRCh37.p13 Human Reference Genome build

Authors

• Andrew Smith
• Jethro Rainford

Development start date: 27th November 2018.

Available at: https://github.com/Fyodir/parsermcparser .

Prerequisites

• Python (3.6.x)
• Modules
  • elementTree (from XML library) (Standard Library)
  • time (Standard Library)
  • requests (2.21.0)
  • pytest (for testing) (4.1.0)
• Working internet connection

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Usage

First run pip install --upgrade -r requirements.txt to ensure that all correct modules are installed on your system prior to use of the fancyparser.py program. If the required modules are not present, the prior command will install them onto your system.

fancyparser.py

Utilises a user input to return an LRG.xml file from the LRG website for use in generating a .bed file.

Input:

Use input of desired LRG number.

Output:

.xml file of queried gene titled "LRG_(LRG number here).xml" (i.e. LRG_1.xml).

.bed file of queried gene titled "LRG_(LRG number)(HGNC nomenclature).bed" (i.e. LRG_1_COL1A1.bed).

Instructions for use:

• Navigate to the /parsermcparser directory on the bash terminal.
• Run the cmd line python3 fancyparser.py.
• You will be prompted with Please enter LRG number: request.
• Enter LRG number of desired query gene (LRG numbers for HGNC names may be found at: https://www.lrg-sequence.org/search/?query=* ).
• The .xml file for the requested LRG and generated .bed file will be returned to the current directory, and may be viewed with a standard text editor.

Example usage:

python3 fancyparser.py [enter]
Please enter LRG number: 39 [enter]

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Testing

• The correct functioning of the parser was determined by the use of assert statements and error generation throughout the script.
• A number of modified, faulty, and corectly formatted test XML files were used to ensure functioning of test features
  • test1.xml, LRG1.xml, LRG_14.xml, LRG_202.xml.
• Assert statements have been included to reject incorrect file types, multiple input LRG numbers, incorrectly formatted / damaged XML files.
• The standard PyTest testing framework was also used to test the whole script for correct functioning (see below).

PyTest

The module "PyTest" was used to test the functionality of the code and to ensure that each function works as intended.

The test files are located within a separate test_files directory.

Usage:

• Ensure you are within the test_files directory.
• Ensure both test_fancyparser.py and test1.xml are present (test.xml is an unmodified copy of the LRG_1.xml, renamed for clarity).
• To invoke testing execute the command pytest -rpf.
• This will search within the directory for the test script and run on the test1.xml file.
• The flags -r (short summary), -p (passed) and -f (fail) are recommended to give a basic visual output of the passed/failed tests, other variables may be found in the relevant man page.