tropicalberto/parsetcgaclinicalxml

a small python program for parsing TCGA clinical XMLs to CSV format

parseTCGAClinicalXML.py

a small python program for parsing TCGA clinical XML files to CSV format table

Install

• Just download parseTCGAClinicalXML.py and put it in the directory where you want to run it.

Run

• run from command line

python parseTCGAClinicalXML.py 'output.csv' 'input_xml_file_list.txt' 'patient'or'followup'or'survival'

replace 'output.csv' with the name you want for your output csv file

'input_xml_file_list.txt' is a text file containing paths to TCGA clinical xml files

use either one of 'patient', 'followup' or 'survival' as the third input variable to output different clinical data of patients.

sample/ directory contains some samples of input and output

• import as a python module and use functions inside parseTCGAClinicalXML.py