Implement an RNA-Sequence Analysis Workflow using DESEQ2. Open a new pull request on a separate branch and comment the PR number here when you're done

[KastanDay]

Implement RNA-Sequence Analysis Workflow as per the following steps.

Quality assess and clean raw sequencing data Align reads to a reference Count the number of reads assigned to each contig/gene Extract counts and store in a matrix Create column metadata table Analyze count data using DESEQ2 Please write and execute the code to do DESEQ2 analysis on the data. If you generate results, please push them to github and mention that in your pull request. Make sure you execute the code, and if it fails keep re-trying with improvements until you get something useful to share.

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

Feel free to comment in this thread to give me additional instructions, or I'll tag you in a comment if I get stuck. If I think I'm successful I'll 'request your review' on the resulting PR. Just watch for emails while I work.

[lil-jr-dev[bot]]

👉 Follow the bot's progress in real time on LangSmith.

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

Feel free to comment in this thread to give me additional instructions, or I'll tag you in a comment if I get stuck. If I think I'm successful I'll 'request your review' on the resulting PR. Just watch for emails while I work.

[lil-jr-dev[bot]]

👉 Follow the bot's progress in real time on LangSmith.

[lil-jr-dev[bot]]

Error in handle_issue_opened: 'CallbackManager' object has no attribute 'raise_error' Traceback

Traceback (most recent call last):
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 255, in handle_event
    if ignore_condition_name is None or not getattr(
AttributeError: 'CallbackManager' object has no attribute 'ignore_chain'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/ai_ta_backend/agents/github_webhook_handlers.py", line 158, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.langsmith_run_id)}})
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/runnables/base.py", line 4064, in invoke
    return self.bound.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 162, in invoke
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 156, in invoke
    self._call(inputs, run_manager=run_manager)
  File "/opt/venv/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/opt/venv/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/_api/deprecation.py", line 145, in warning_emitting_wrapper
    return wrapped(*args, **kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 543, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/_api/deprecation.py", line 145, in warning_emitting_wrapper
    return wrapped(*args, **kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 363, in __call__
    return self.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 162, in invoke
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 156, in invoke
    self._call(inputs, run_manager=run_manager)
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1391, in _call
    next_step_output = self._take_next_step(
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1097, in _take_next_step
    [
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1097, in <listcomp>
    [
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1182, in _iter_next_step
    yield self._perform_agent_action(
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1204, in _perform_agent_action
    observation = tool.run(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/tools.py", line 401, in run
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/tools.py", line 358, in run
    self._run(*tool_args, run_manager=run_manager, **tool_kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain_community/tools/vectorstore/tool.py", line 57, in _run
    return chain.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 149, in invoke
    run_manager = callback_manager.on_chain_start(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 1296, in on_chain_start
    handle_event(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 285, in handle_event
    if handler.raise_error:
AttributeError: 'CallbackManager' object has no attribute 'raise_error'