horrible regex abuse i used to get the analysis ids corresponding to pipeline outputs

get_analysis_ids.py

import os
import re


xml_file = sys.argv[1]

tree = ET.parse(xml_file)

root = tree.getroot()

def munge(root):
    res = []
    for result in root.iter("Result"):
        for a in result.find("files"):
            fname = a.find("filename").text
            munged = fname.split(".")[2]
            res.append(munged)
    return res

def pair(root, files):
    ffiles = []
    ids = []
    for f in files:
        print f
        num = re.search("([0-9])$", f).groups()[0]
        try:
            bases = "_" + re.search("([ACGT]{6,6})", f).groups()[0]
        except:
            bases = ""
        newre = re.sub("XX_.*", "", f) + ".*" + num + bases
        print newre
        for result in root.iter("Result"):
            aid = result.find("analysis_id").text
            a = result.find("files")[0]
            fname = a.find("filename").text
            munged = fname.split(".")[2]
            if re.search(newre, munged) is not None:
                print (f, aid)
                ffiles.append(f)
                ids.append(aid)
                break
        else:
            print "no matching analysis found for " + f
            print munged, newre, f
            return ffiles, ids
    return ffiles, ids