Python Decompile APK using ApkTool and Subprocess

I am builing a Python Application that decompiles Android APK makes some modifications and recompiles it.

Here is the code:

from shutil import copyfile

# Copy the APK to the output directory.
copyfile('./source/rat.apk', './output/rat.apk')

# Decompiles the APK.
subprocess.call(['apktool','d','./output/rat.apk','-f'], stdout=FNULL, stderr=subprocess.STDOUT)

# Modifies address and port.
with open('./output/RAT/app/src/main/res/values/strings.xml','w+') as netaddress:
    address = netaddress.read()
    address.replace('youraddress','x')
    address.replace('yourport','8080')
    netaddress.write(address)
    print(netaddress.read())
    netaddress.close()

# Recompiles it.
subprocess.call(['apktool','b','./output/RAT'], stdout=FNULL, stderr=subprocess.STDOUT)

But it throws this Exception when running:

with open('./output/RAT/app/src/main/res/values/strings.xml','w+') as netaddress:
FileNotFoundError: [Errno 2] No such file or directory: './output/RAT/app/src/main/res/values/strings.xml'

Update:
When i try to use the command apktool d source/rat.apk

This is the output i receive:

18:45:51 up 1 min,  0 users,  load average: 0.52, 0.58, 0.59
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
I: Using Apktool 2.0.2-dirty on rat.apk
I: Loading resource table...
I: Decoding AndroidManifest.xml with resources...
I: Loading resource table from file: /home/stecco/apktool/framework/1.apk
W: Could not decode attr value, using undecoded value instead: ns=android, name=versionCode, value=0x00000001
I: Loading resource table from file: /home/stecco/apktool/framework/1.apk
W: Could not decode attr value, using undecoded value instead: ns=android, name=versionName, value=0x00000014
I: Loading resource table from file: /home/stecco/apktool/framework/1.apk
W: Could not decode attr value, using undecoded value instead: ns=android, name=versionCode, value=0x00000001
I: Loading resource table from file: /home/stecco/apktool/framework/1.apk
W: Could not decode attr value, using undecoded value instead: ns=android, name=versionName, value=0x00000014
Exception in thread "main" java.lang.NullPointerException
        at java.io.Writer.write(Writer.java:157)
        at brut.androlib.res.util.ExtMXSerializer.writeAttributeValue(ExtMXSerializer.java:38)
        at org.xmlpull.mxp1_serializer.MXSerializer.attribute(MXSerializer.java:696)
        at org.xmlpull.v1.wrapper.classic.XmlSerializerDelegate.attribute(XmlSerializerDelegate.java:106)
        at org.xmlpull.v1.wrapper.classic.StaticXmlSerializerWrapper.writeStartTag(StaticXmlSerializerWrapper.java:267)
        at org.xmlpull.v1.wrapper.classic.StaticXmlSerializerWrapper.event(StaticXmlSerializerWrapper.java:211)
        at brut.androlib.res.decoder.XmlPullStreamDecoder$1.event(XmlPullStreamDecoder.java:83)
        at brut.androlib.res.decoder.XmlPullStreamDecoder.decode(XmlPullStreamDecoder.java:141)
        at brut.androlib.res.decoder.XmlPullStreamDecoder.decodeManifest(XmlPullStreamDecoder.java:153)
        at brut.androlib.res.decoder.ResFileDecoder.decodeManifest(ResFileDecoder.java:140)
        at brut.androlib.res.AndrolibResources.decodeManifestWithResources(AndrolibResources.java:199)
        at brut.androlib.Androlib.decodeManifestWithResources(Androlib.java:140)
        at brut.androlib.ApkDecoder.decode(ApkDecoder.java:100)
        at brut.apktool.Main.cmdDecode(Main.java:165)
        at brut.apktool.Main.main(Main.java:81)

Solved every problem by installing Apktool 2.4.0 it seems that the version 2.0.2 it's really buggy and even 2.2.2 and 2.3.2.

But another problem came up when i try to recompile it it gives me a classes.dex not an apk how can i solve this?

FileNotFoundError is an explicit name which means that a function of your code cannot find this file. Without more details about where this exception happens, the only answer i can give you is to verify that :

1. the directory "./output/" exist
2. the file is correctly created after copying it with shutil