handling fasta files with biopython #202
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Pull request overview
This pull request refactors FASTA file parsing by replacing manual string manipulation with BioPython's SeqIO library. The change improves code maintainability and robustness by using a well-tested, standard library for biological sequence format handling.
Key Changes:
- Replaced manual line-by-line FASTA parsing with BioPython's
SeqIO.parse() - Added biopython 1.84 dependency to requirements.txt
- Simplified header matching logic using BioPython's record.id and record.description attributes
Reviewed changes
Copilot reviewed 2 out of 3 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| requirements.txt | Added biopython==1.84 dependency |
| worker.py | Added imports for BioPython and StringIO (not used in this file) |
| helpers.py | Replaced manual FASTA parsing with BioPython's SeqIO.parse in check_for_sequence_data function |
Comments suppressed due to low confidence (2)
worker.py:6
- Import of 'StringIO' is not used.
from io import StringIO
worker.py:7
- Import of 'SeqIO' is not used.
from Bio import SeqIO
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| return False, f"Empty sequence found for header: {fasta_header}" | ||
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| # Reconstruct FASTA format for storage | ||
| sequence_data = f">{sequence_found.description}\n{str(sequence_found.seq)}" |
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Minor behavioral change: The BioPython implementation returns the sequence as a single unwrapped line, whereas the original implementation preserved line breaks from the source file. While both are valid FASTA format, if line wrapping is desired (typically 60-80 characters per line), consider using textwrap.fill() or BioPython's SeqIO.write() to wrap the sequence.
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| if not sequence_data.strip(): | ||
| return False, f"No sequence data found for isolate '{isolate_sample_id}'" |
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This check is now redundant. Since sequence_found is guaranteed to be non-None (line 1100) and have a non-empty sequence (line 1104), the reconstructed sequence_data at line 1108 will always contain content and never be empty. Consider removing this check.
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Co-authored-by: Copilot <[email protected]>
Co-authored-by: Copilot <[email protected]>
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@desafinadude I've opened a new pull request, #203, to work on those changes. Once the pull request is ready, I'll request review from you. |
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@desafinadude I've opened a new pull request, #204, to work on those changes. Once the pull request is ready, I'll request review from you. |
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