py-gbcms 2.0.0__py3-none-any.whl

gbcms/config.py

@@ -0,0 +1,98 @@
+"""Configuration classes and enums for GetBaseCounts."""
+
+import os
+from dataclasses import dataclass
+from enum import IntEnum
+
+
+class CountType(IntEnum):
+    """Enumeration for different count types."""
+
+    DP = 0  # Total depth
+    RD = 1  # Reference depth
+    AD = 2  # Alternate depth
+    DPP = 3  # Positive strand depth
+    RDP = 4  # Positive strand reference depth
+    ADP = 5  # Positive strand alternate depth
+    DPF = 6  # Fragment depth
+    RDF = 7  # Fragment reference depth
+    ADF = 8  # Fragment alternate depth
+
+
+@dataclass
+class Config:
+    """Configuration for base counting."""
+
+    fasta_file: str
+    bam_files: dict[str, str]  # sample_name -> bam_path
+    variant_files: list[str]
+    output_file: str
+
+    # Optional parameters
+    mapping_quality_threshold: int = 20
+    base_quality_threshold: int = 0
+    filter_duplicate: bool = True
+    filter_improper_pair: bool = False
+    filter_qc_failed: bool = False
+    filter_indel: bool = False
+    filter_non_primary: bool = False
+    output_positive_count: bool = True
+    output_negative_count: bool = False
+    output_fragment_count: bool = False
+    fragment_fractional_weight: bool = False
+    max_block_size: int = 10000
+    max_block_dist: int = 100000
+    num_threads: int = 1
+    backend: str = "joblib"  # Parallelization backend
+    input_is_maf: bool = False
+    input_is_vcf: bool = False
+    output_maf: bool = False
+    generic_counting: bool = False
+    max_warning_per_type: int = 3
+
+    def __post_init__(self) -> None:
+        """Validate configuration."""
+        if not os.path.exists(self.fasta_file):
+            raise FileNotFoundError(f"Reference FASTA file not found: {self.fasta_file}")
+
+        fai_file = f"{self.fasta_file}.fai"
+        if not os.path.exists(fai_file):
+            raise FileNotFoundError(
+                f"Reference FASTA index not found: {fai_file}. "
+                f"Please index with: samtools faidx {self.fasta_file}"
+            )
+
+        for sample, bam_path in self.bam_files.items():
+            if not os.path.exists(bam_path):
+                raise FileNotFoundError(f"BAM file not found for sample {sample}: {bam_path}")
+
+            # Check for BAM index
+            bai_file1 = bam_path.replace(".bam", ".bai")
+            bai_file2 = f"{bam_path}.bai"
+            if not os.path.exists(bai_file1) and not os.path.exists(bai_file2):
+                raise FileNotFoundError(
+                    f"BAM index not found for {bam_path}. "
+                    f"Please index with: samtools index {bam_path}"
+                )
+
+        for variant_file in self.variant_files:
+            if not os.path.exists(variant_file):
+                raise FileNotFoundError(f"Variant file not found: {variant_file}")
+
+        if self.input_is_maf and self.input_is_vcf:
+            raise ValueError("--maf and --vcf are mutually exclusive")
+
+        if not self.input_is_maf and not self.input_is_vcf:
+            raise ValueError("Either --maf or --vcf must be specified")
+
+        if self.input_is_vcf and self.output_maf:
+            raise ValueError("--omaf can only be used with --maf input")
+
+        if self.num_threads < 1:
+            raise ValueError("Number of threads must be at least 1")
+
+        if self.max_block_size < 1:
+            raise ValueError("max_block_size must be at least 1")
+
+        if self.max_block_dist < 1:
+            raise ValueError("max_block_dist must be at least 1")