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-[metadata] -lock-version = "2.1" -python-versions = ">=3.9" -content-hash = "7dcf5e43173ccebb51625949b121295163b1ca193a641199e0b113404731f414" diff --git a/pyproject.toml b/pyproject.toml index 1bd6ec6..fab575e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "gene-fetch" -version = "1.0.20" +version = "1.0.21" description = "Gene Fetch: High-throughput NCBI Sequence Retrieval Tool" authors = ["D. Parsons , B. Price "] license = "MIT" diff --git a/src/gene_fetch/__init__.py b/src/gene_fetch/__init__.py index 20d20a5..1231c89 100644 --- a/src/gene_fetch/__init__.py +++ b/src/gene_fetch/__init__.py @@ -5,7 +5,7 @@ using sample taxonomic information. """ -__version__ = "1.0.20" +__version__ = "1.0.21" from .core import Config from .entrez_handler import EntrezHandler diff --git a/src/gene_fetch/__pycache__/__init__.cpython-312.pyc b/src/gene_fetch/__pycache__/__init__.cpython-312.pyc deleted file mode 100644 index 5e1cb0e..0000000 Binary files a/src/gene_fetch/__pycache__/__init__.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/__init__.cpython-313.pyc b/src/gene_fetch/__pycache__/__init__.cpython-313.pyc deleted file mode 100644 index 085fd8f..0000000 Binary files a/src/gene_fetch/__pycache__/__init__.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/core.cpython-312.pyc b/src/gene_fetch/__pycache__/core.cpython-312.pyc deleted file mode 100644 index af27330..0000000 Binary files a/src/gene_fetch/__pycache__/core.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/core.cpython-313.pyc b/src/gene_fetch/__pycache__/core.cpython-313.pyc deleted file mode 100644 index c8dadce..0000000 Binary files a/src/gene_fetch/__pycache__/core.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/entrez_handler.cpython-312.pyc b/src/gene_fetch/__pycache__/entrez_handler.cpython-312.pyc deleted file mode 100644 index f706959..0000000 Binary files a/src/gene_fetch/__pycache__/entrez_handler.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/entrez_handler.cpython-313.pyc b/src/gene_fetch/__pycache__/entrez_handler.cpython-313.pyc deleted file mode 100644 index a395d5a..0000000 Binary files a/src/gene_fetch/__pycache__/entrez_handler.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/main.cpython-312.pyc b/src/gene_fetch/__pycache__/main.cpython-312.pyc deleted file mode 100644 index 2e2865c..0000000 Binary files a/src/gene_fetch/__pycache__/main.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/main.cpython-313.pyc b/src/gene_fetch/__pycache__/main.cpython-313.pyc deleted file mode 100644 index 2d82a0c..0000000 Binary files a/src/gene_fetch/__pycache__/main.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/output_manager.cpython-312.pyc b/src/gene_fetch/__pycache__/output_manager.cpython-312.pyc deleted file mode 100644 index b1476e0..0000000 Binary files a/src/gene_fetch/__pycache__/output_manager.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/output_manager.cpython-313.pyc b/src/gene_fetch/__pycache__/output_manager.cpython-313.pyc deleted file mode 100644 index 1dc8460..0000000 Binary files a/src/gene_fetch/__pycache__/output_manager.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/processors.cpython-312.pyc b/src/gene_fetch/__pycache__/processors.cpython-312.pyc deleted file mode 100644 index 3e0eebd..0000000 Binary files a/src/gene_fetch/__pycache__/processors.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/processors.cpython-313.pyc b/src/gene_fetch/__pycache__/processors.cpython-313.pyc deleted file mode 100644 index 43a0c98..0000000 Binary files a/src/gene_fetch/__pycache__/processors.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/sequence_processor.cpython-312.pyc b/src/gene_fetch/__pycache__/sequence_processor.cpython-312.pyc deleted file mode 100644 index 4e0dd9e..0000000 Binary files a/src/gene_fetch/__pycache__/sequence_processor.cpython-312.pyc and /dev/null differ diff --git a/src/gene_fetch/__pycache__/sequence_processor.cpython-313.pyc b/src/gene_fetch/__pycache__/sequence_processor.cpython-313.pyc deleted file mode 100644 index 7210197..0000000 Binary files a/src/gene_fetch/__pycache__/sequence_processor.cpython-313.pyc and /dev/null differ diff --git a/src/gene_fetch/core.py b/src/gene_fetch/core.py index 8cb8ce6..f810026 100644 --- a/src/gene_fetch/core.py +++ b/src/gene_fetch/core.py @@ -288,6 +288,8 @@ def __init__(self, email, api_key): "psbA": "psba", "trnh-psba": "psba", "psba-trnh": "psba", + "lsu": "28s", + "ssu": "18s", } # Define gene type categories @@ -329,7 +331,7 @@ def __init__(self, email, api_key): "28S rRNA[Gene]", "rrn28[Gene]", "LSU rRNA[Gene]", - "28S ribosomal RNA[rRNA]" + "28S ribosomal RNA[rRNA]", "28S rRNA[rRNA]", "LSU rRNA[rRNA]", "rrn28[rRNA]", diff --git a/src/gene_fetch/sequence_processor.py b/src/gene_fetch/sequence_processor.py index 93c728a..3099f17 100644 --- a/src/gene_fetch/sequence_processor.py +++ b/src/gene_fetch/sequence_processor.py @@ -208,7 +208,7 @@ def extract_nucleotide( variations = self.config._protein_coding_genes[base_gene] gene_variations = {v.split("[")[0].strip('"').lower() for v in variations} - # Add common pattern variations for different writing styles + # Common pattern variations for different naming conventions if base_gene == "rbcl": pattern_variations = [ "rbcl", @@ -333,6 +333,17 @@ def extract_nucleotide( "rrn16", "rrn 16", ] + elif base_gene == "12s" or base_gene == "12s rrna" or base_gene == "rrn12": + pattern_variations = [ + "12s", + "12s rrna", + "12s ribosomal rna", + "12s ribosomal", + "12 s rrna", + "12 s", + "rrn12", + "rrn 12" + ] elif base_gene == "18s" or base_gene == "18s rrna" or base_gene == "rrn18": pattern_variations = [ "18s", @@ -1049,7 +1060,7 @@ def try_fetch_at_taxid( # Get summaries and sort by length try: sorted_summaries = [] - batch_size = 200 + batch_size = 500 for i in range(0, len(id_list), batch_size): batch_ids = id_list[i : i + batch_size] @@ -1093,9 +1104,9 @@ def try_fetch_at_taxid( key=lambda x: x[1], reverse=True ) - # Take only top 250 IDs by sequence length + # Take only top 10 IDs by sequence length (provides fallback if some records are invalid) processed_ids = [ - item[0] for item in sorted_summaries[:250] + item[0] for item in sorted_summaries[:10] ] logger.info( f"Successfully filtered to top proteins by length (longest: {sorted_summaries[0][1]} aa)" @@ -1351,9 +1362,9 @@ def try_fetch_at_taxid( key=lambda x: x[1], reverse=True ) - # Take only top 250 IDs by sequence length + # Take only top 10 IDs by sequence length (provides fallback if some records are invalid) processed_ids = [ - item[0] for item in sorted_summaries[:250] + item[0] for item in sorted_summaries[:10] ] logger.info( f"Successfully filtered to top nucleotide sequences by length (longest: {sorted_summaries[0][1]} bp)" @@ -1771,11 +1782,12 @@ def extract_rRNA(self, record, gene_name, single_mode=False): # Define alternative names for different rRNA types rRNA_alternatives = { - "16s": ["16s", "rrs", "rrn16", "ssu", "small subunit"], # Small subunit bacterial + "16s": ["16s", "rrs", "rrn16", "ssu", "small subunit", "s-rrna"], # Small subunit bacterial "18s": ["18s", "rrn18", "ssu", "small subunit"], # Small subunit eukaryotic - "23s": ["23s", "rrl", "rrn23", "lsu", "large subunit"], # Large subunit bacterial - "28s": ["28s", "rrn28", "lsu", "large subunit"], # Large subunit eukaryotic - "12s": ["12s", "mt-rrn1", "mt 12s"], # Mitochondrial SSU + "23s": ["23s", "rrl", "rrn23", "lsu", "large subunit", "l-rrna"], # Large subunit bacterial + "28s": ["28s", "rrn28", "lsu", "large subunit", "l-rrna"], # Large subunit eukaryotic + "12s": ["12s", "mt-rrn1", "mt-rnr1", "mt 12s", "s-rrna"], # Mitochondrial SSU + "16s": ["16s", "mt-rrn2", "mt-rnr2", "mt 16s", "l-rrna"], # Mitochondrial LSU "5s": ["5s", "rrn5", "rrn5s", "rrna 5s"], # 5S bacterial }