dnachisel not working on AWS Lambda

Importing the library doesn’t seem to work in AWS Lambda.

Something like the following:

import dnachisel as dc

def lambda_handler(event, context):  
    return "test"

When run on lambda throws:

{
  "errorMessage": "Unable to import module 'lambda_function': cannot import name '_aligners' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/var/task/Bio/Align/__init__.py)",
  "errorType": "Runtime.ImportModuleError",
  "stackTrace": []
}

Everything works fine if I mock the lambda locally. I uploaded the lambda code and the dependencies as a zip file, but also tried uploading dnachisel as a lambda layer and got the same error.

Python version: 3.8 dnachisel version: 3.2.9

[guzmanvig]

Unfortunately we can’t use code build as it would imply changing the whole infrastructure of our project. However, you are right, the problem is with biopython. I tried the following code and got the same issue.

from Bio.Align import _aligners

def lambda_handler(event, context):
    return "test"

Thank you!

[veghp]

I have one more suggestion. I believe this problem is not related to DNA Chisel, but Biopython.

When we import /site-packages/Bio/Align/__init__.py it starts with

import sys

from Bio.Align import _aligners

which is the line that causes problem according to your error. This is an .so file, and these discussions suggest “Problem is solved by deploying the package through AWS codeBuild”:

https://stackoverflow.com/questions/64450587/error-trying-to-import-pysftp-in-lambda-cannot-import-name-bcrypt-from-parti

https://github.com/pymupdf/PyMuPDF/issues/430#issuecomment-576231408