Python script for merging optical map xml files (for different scaffolds) into one large xml file

merge_optical_map_xml_files.py

import sys
import os
from xml.etree import ElementTree as ET
import AvrilFileUtils

class Error (Exception): pass

#====================================================================#

# define a function to merge optical map xml files for different scaffolds.

def merge_optical_map_xml_files(input_file_list, output_xml_file):
    """Merge the optical map xml files in a directory into one output xml file"""

    # get a list of all the input files:
    filenames = []
    fileObj = open(input_file_list, "r")
    for line in fileObj:
        line = line.rstrip()
        temp = line.split()
        filename = temp[0]
        filenames.append(filename)
    fileObj.close()

    # combine all the xml files:
    # copied code from https://gist.github.com/cgoldberg/4320815:
    seen_experiment = False
    cases = []
    for filename in filenames:
        print("reading filename %s" % filename) 
        tree = ET.parse(filename)
        root = tree.getroot() # 'aligned_maps_document'
        for child in root:
            if child.tag == 'experiment':
                if seen_experiment == True:
                    root.remove(child)
                else:
                # keep one 'experiment' child. Note: I think this is necessary to write out the data with ElementTree
                    seen_experiment = True
        cases.append(root.getchildren())  
    
    # write out the new tree:
    new_root = ET.Element('aligned_maps_document')
    for case in cases:
        new_root.extend(case)
    new_tree = ET.ElementTree(new_root)
    # see comments at http://stackoverflow.com/questions/12612648/python-element-tree-is-removing-the-xml-declaration
    new_tree.write(output_xml_file, encoding="iso-8859-1", xml_declaration=True, method="xml")

    # open the output xml file, so we can append a new line character (for some reason the
    # ElementTree object does not seem to end the file with a new line character):
    outputfileObj = open(output_xml_file, "a")
    outputfileObj.write('\n')
    outputfileObj.close()
    
    return
        
#====================================================================#

# define a function to rewrite the header of 'output_xml_file', so that
# it can be read by MapSolver

def rewrite_optical_map_xml_header(temp_output_xml_file, output_xml_file):
    """rewrite the header of the optical map xml file, so that it can be read by MapSolver"""
    
    # open the output file:
    outputfileObj = open(output_xml_file, "w")
    # write the header in the output file:
    outputfileObj.write('<?xml version="1.0" encoding="iso-8859-1"?>\n')
    outputfileObj.write('<!-- @version:0.1 -->\n\n')
    outputfileObj.write('<!-- this is a comment -->\n')
    outputfileObj.write('<aligned_maps_document version="0.5">\n\n')
    outputfileObj.write('<experiment>\n')
    
    # read in temp_output_xml_file:
    found_start = False
    fileObj = open(temp_output_xml_file, "r")
    for line in fileObj:
        if '<creator>gentig2</creator>' in line:
            found_start = True
        if found_start == True:
            outputfileObj.write(line)
    fileObj.close()
    outputfileObj.close()
        
#====================================================================#

def main():
    
    # check the command-line arguments:
    if len(sys.argv) != 3 or os.path.exists(sys.argv[1]) == False:
        print("Usage: %s input_file_list output_xml_file" % sys.argv[0]) 
        sys.exit(1)
    input_file_list = sys.argv[1]
    output_xml_file = sys.argv[2]

    # merge the optical map xml files for different scaffolds:
    temp_output_xml_file = AvrilFileUtils.make_filename(os.getcwd())
    merge_optical_map_xml_files(input_file_list, temp_output_xml_file)
    
    # rewrite the header of the 'output_xml_file' file so that it can be read by MapSolver:
    rewrite_optical_map_xml_header(temp_output_xml_file, output_xml_file)
    
    # delete temporary files:
    os.unlink(temp_output_xml_file)
    
#====================================================================#

if __name__=="__main__":
    main()

#====================================================================#