reportwriter.py

#!/usr/bin/env python3

import xml.etree.ElementTree as ET
from itertools import islice

def writeReport(xmlfile, dataType, numDown, seqType):
    
    # create element tree object
    tree = ET.parse(xmlfile)
    # get root element
    root = tree.getroot()
    
    # gather info for report file
    accessID = []
    title = []
    enaURL = []

    if dataType == "run":
        if numDown:
            for item in islice(root.iterfind("RUN/IDENTIFIERS/PRIMARY_ID"), 0, int(numDown)):
                accessID.append(item.text)
            for item in islice(root.iter("TITLE"), 0, int(numDown)):
                title.append(item.text)
        else:
            for item in root.iterfind("RUN/IDENTIFIERS/PRIMARY_ID"):
                accessID.append(item.text)
            for item in root.iter("TITLE"):
                title.append(item.text)
    elif dataType == "study":
        if numDown:
            for item in islice(root.iterfind("STUDY/IDENTIFIERS/PRIMARY_ID"), 0, int(numDown)):
                accessID.append(item.text)
            for item in islice(root.iter("STUDY_TITLE"), 0, int(numDown)):
                title.append(item.text)
        else:
            for item in root.iterfind("STUDY/IDENTIFIERS/PRIMARY_ID"):
                accessID.append(item.text)
            for item in root.iter("STUDY_TITLE"):
                title.append(item.text)
    elif dataType == "experiment":
        if numDown:
            for item in islice(root.iterfind("EXPERIMENT/IDENTIFIERS/PRIMARY_ID"), 0, int(numDown)):
                accessID.append(item.text)
            for item in islice(root.iter("TITLE"), 0, int(numDown)):
                title.append(item.text)
        else:
            for item in root.iterfind("EXPERIMENT/IDENTIFIERS/PRIMARY_ID"):
                accessID.append(item.text)
            for item in root.iter("TITLE"):
                title.append(item.text)
    elif dataType == "sample":
        if numDown:
            for item in islice(root.iterfind("SAMPLE/IDENTIFIERS/PRIMARY_ID"), 0, int(numDown)):
                accessID.append(item.text)
            for item in islice(root.iter("TITLE"), 0, int(numDown)):
                title.append(item.text)
        else:
            for item in root.iterfind("SAMPLE/IDENTIFIERS/PRIMARY_ID"):
                accessID.append(item.text)
            for item in root.iter("TITLE"):
                title.append(item.text)

    for item in accessID:
        enaURL.append("https://www.ebi.ac.uk/ena/browser/view/{0}".format(item))

    # write report file
    with open('report.txt', 'w') as outfile:
        for item in zip(accessID, title, seqType, enaURL):
            outfile.write("{0}\t{1}\t{2}\t{3}\n".format(item[0], item[1], item[2], item[3]))