fix: Add more FASTA extensions #49
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Sequence Diagram(s)sequenceDiagram
participant User
participant get_format
User->>get_format: Call with file path
get_format->>get_format: Check file extension against updated FASTA extensions list and compression types
get_format-->>User: Return "fasta" if match, else other format or error
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🧰 Additional context used📓 Path-based instructions (1)`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
🪛 Ruff (0.11.9)snakemake_wrapper_utils/snakemake.py38-41: Use ternary operator Replace (SIM108) 🔇 Additional comments (3)
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snakemake_wrapper_utils/snakemake.py (1)
45-47: Improve maintainability with constants and case-insensitive matching
To simplify updates and avoid missing uppercase variants (e.g..FA), normalizeextto lowercase and extract FASTA/FASTQ extension sets to module‐level constants. For example:@@ get_format(path) - if exts[-1] in (".gz", ".bgz", ".bz2"): + if exts[-1] in (".gz", ".bgz", ".bz2"): ext = exts[-2] else: ext = exts[-1] + ext = ext.lower() - if ext in (".fq", ".fastq"): + if ext in FASTQ_EXTS: return "fastq" - elif ext in (".fa", ".fas", ".fna", ".ffn", ".faa", ".fasta", ".mpfa", ".frn"): - # https://en.wikipedia.org/wiki/FASTA_format - return "fasta" + elif ext in FASTA_EXTS: + return "fasta"And at the top of the file:
# Supported file extensions for FASTA/FASTQ formats: FASTA_EXTS = {".fa", ".fas", ".fna", ".ffn", ".faa", ".fasta", ".mpfa", ".frn"} # https://en.wikipedia.org/wiki/FASTA_format FASTQ_EXTS = {".fq", ".fastq"}
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snakemake_wrapper_utils/snakemake.py(2 hunks)
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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
snakemake_wrapper_utils/snakemake.py
🔇 Additional comments (1)
snakemake_wrapper_utils/snakemake.py (1)
45-47: Extended FASTA extensions added
The new extensions.ffn,.faa,.mpfa, and.frnaccurately reflect the FASTA variants, and the Wikipedia URL comment provides valuable context for future maintainers.
Fixes #48
Summary by CodeRabbit
New Features
.ffn,.faa,.mpfa, and.frn..xzcompression extension alongside existing ones.Documentation