********************************************************************************
Step 1
********************************************************************************

------Action------
THOUGHT:
None
ACTION TYPE:
None
ACTION CONTENT:
None

-----Response-----
RESPONSE (User Message):
USER QUERY: Check if the DNA sequence 'AGCTTX' is valid, and if so, transcribe it to mRNA and translate that to an amino acid sequence. Otherwise, answer 'Invalid DNA sequence'.
Save the final answer in the variable `final_answer`.

Use the code base located at `/root/m3eval/m3eval` to solve this query. Your current directory is `/root/playground`.

If the import path in retrieved code block says `testing/dir_name/file_name.py` and you want to import variable, function or class called `obj` from this file, then import using `from testing.dir_name.file_name import obj`.

The code base path has either been installed via pip or has been already been added to the system path via
```
import sys
sys.path.extend(['/root/m3eval'])
```

********************************************************************************
Step 2
********************************************************************************

------Action------
THOUGHT:
Before writing any code, I need to search for functions in the `dna_sequencer.py` file that can validate a DNA sequence and transcribe it to mRNA. I will also look for a function that can translate mRNA to an amino acid sequence. I will start by searching for functions related to DNA sequence validation.
ACTION TYPE:
search
ACTION CONTENT:
(type: FUNCTION) AND (file_path: *\/dna_sequencer.py) AND (text: validate)

-----Response-----
RESPONSE (Retrieval Result):
QUERY:
(type: FUNCTION) AND (file_path: *\/dna_sequencer.py) AND (text: validate)

CODE BLOCKS:
---
file_path=m3eval/dna_sequencer.py
lines=[24, 26]
type=FUNCTION
content={
def is_valid_dna_sequence(dna_sequence):
    return set(dna_sequence).issubset(set('ACGT'))
}
---
file_path=m3eval/dna_sequencer.py
lines=[5, 8]
type=FUNCTION
content={
def transcribe_dna_to_mrna(dna_sequence):
    transcription_map = str.maketrans('ACGT', 'UGCA')
    return dna_sequence.translate(transcription_map)
}
---
file_path=m3eval/dna_sequencer.py
lines=[28, 31]
type=FUNCTION
content={
def reverse_transcribe_mrna_to_dna(mrna_sequence):
    reverse_transcription_map = str.maketrans('UCAG', 'AGTC')
    return mrna_sequence.translate(reverse_transcription_map)
}
---
(1 additional code blocks not shown. Search again with the same query to see additional results.)

Prototypes for the next 1 out of 1 classes/functions found in unexpanded results (search again with the same query to see details):
def translate_mrna_to_amino_acid(mrna_sequence): ... # m3eval/dna_sequencer.py

********************************************************************************
Step 3
********************************************************************************

------Action------
THOUGHT:
The `is_valid_dna_sequence` function can be used to validate the DNA sequence. The `transcribe_dna_to_mrna` function can transcribe DNA to mRNA. There is also a mention of a `translate_mrna_to_amino_acid` function, which I assume can translate mRNA to an amino acid sequence. I will search again with the same query to retrieve the implementation of the `translate_mrna_to_amino_acid` function.
ACTION TYPE:
search
ACTION CONTENT:
(type: FUNCTION) AND (file_path: *\/dna_sequencer.py) AND (text: translate_mrna_to_amino_acid)

-----Response-----
RESPONSE (Retrieval Result):
QUERY:
(type: FUNCTION) AND (file_path: *\/dna_sequencer.py) AND (text: translate_mrna_to_amino_acid)

CODE BLOCKS:
---
file_path=m3eval/dna_sequencer.py
lines=[10, 15]
type=FUNCTION
content={
def translate_mrna_to_amino_acid(mrna_sequence):
    # Simplified codon to amino acid mapping
    codon_map = {'AUG': 'Methionine', 'UUU': 'Phenylalanine', 'UUC': 'Phenylalanine'}
    amino_acids = [codon_map.get(mrna_sequence[i:i+3], 'X') for i in range(0, len(mrna_sequence), 3)]
    return '-'.join(amino_acids)
}
---
file_path=m3eval/dna_sequencer.py
lines=[0, 3]
type=FUNCTION
content={
def count_nucleotides(dna_sequence):
    from collections import Counter
    return dict(Counter(dna_sequence))
}
---
(All code blocks matching the query were returned.)

********************************************************************************
Step 4
********************************************************************************

------Action------
THOUGHT:
I have retrieved the `translate_mrna_to_amino_acid` function which can be used to translate mRNA to an amino acid sequence. Now I will write the code to check if the given DNA sequence 'AGCTTX' is valid using the `is_valid_dna_sequence` function. If it is valid, I will transcribe it to mRNA using `transcribe_dna_to_mrna` and then translate that to an amino acid sequence using `translate_mrna_to_amino_acid`. The result will be stored in the variable `final_answer`.
ACTION TYPE:
code
ACTION CONTENT:
from m3eval.dna_sequencer import is_valid_dna_sequence, transcribe_dna_to_mrna, translate_mrna_to_amino_acid

# Given DNA sequence
dna_sequence = 'AGCTTX'

# Check if the DNA sequence is valid
if is_valid_dna_sequence(dna_sequence):
    # Transcribe the valid DNA sequence to mRNA
    mrna_sequence = transcribe_dna_to_mrna(dna_sequence)
    # Translate the mRNA sequence to an amino acid sequence
    final_answer = translate_mrna_to_amino_acid(mrna_sequence)
else:
    final_answer = 'Invalid DNA sequence'

-----Response-----
RESPONSE (Execution Result):
CODE EXECUTED WITHOUT ERROR, STDOUT WAS EMPTY
RELEVANT VARIABLES (only shown if string rep. has changed after code exec):
{"is_valid_dna_sequence": <function is_valid_dna_sequence at 0x7f89ac459e40>, "transcribe_dna_to_mrna": <function transcribe_dna_to_mrna at 0x7f89ac45a0c0>, "translate_mrna_to_amino_acid": <function translate_mrna_to_amino_acid at 0x7f89ac45a020>, "dna_sequence": AGCTTX, "final_answer": Invalid DNA sequence}

********************************************************************************
Step 5
********************************************************************************

------Action------
THOUGHT:
The code executed without error and the `final_answer` variable indicates that the DNA sequence 'AGCTTX' is invalid. The task is completed successfully.
ACTION TYPE:
done
ACTION CONTENT:
True

-----Response-----
None