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import tempfile
from pathlib import Path
from typing import Optional, List
# This is a placeholder for the MCP decorator.
# In a real MCP environment, this would be provided by the MCP framework.
def tool(func):
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
mcp = type("mcp", (), {"tool": tool})
@mcp.tool
def bbmap(
in_file: Path,
ref_file: Path,
out_file: Path,
in2_file: Optional[Path] = None,
out_unmapped: Optional[Path] = None,
java_memory: Optional[str] = None,
threads: Optional[int] = None,
overwrite: bool = False,
interleaved: str = "auto",
reads: int = -1,
samplerate: float = 1.0,
bamscript: Optional[Path] = None,
scafstats: Optional[Path] = None,
covstats: Optional[Path] = None,
fast: bool = False,
slow: bool = False,
vslow: bool = False,
max_indel: int = 16000,
min_identity: float = 0.76,
min_hits: int = 1,
local_alignment: bool = False,
perfect_mode: bool = False,
ambiguous_reads_mode: str = "best",
sam_version: str = "1.4",
secondary_alignments: bool = True,
max_sites: int = 5,
pairlen: int = 32000,
qtrim: str = "f",
untrim: bool = False,
trimq: int = 6,
min_avg_quality: int = 0,
nodisk: bool = False,
) -> dict:
"""
Maps sequencing reads to a reference genome using BBMap.
BBMap is a fast and accurate splice-aware read mapper. This tool wraps the
bbmap.sh script, providing a comprehensive set of parameters for fine-tuning
the mapping process.
Args:
in_file: Path to the primary input file (fasta, fastq, sam; compressed or uncompressed).
ref_file: Path to the reference genome file (fasta).
out_file: Path for the output SAM file.
in2_file: Path to the second input file for paired-end reads.
out_unmapped: Path to write unmapped reads to.
java_memory: Java heap size (e.g., '8g', '1000m'). Passed as -Xmx to the JVM.
threads: Number of threads to use. If not set, BBMap will auto-detect.
overwrite: If True, allows overwriting of existing output files.
interleaved: Set to 't' or 'f' if reads are interleaved; 'auto' detects.
reads: If positive, quit after processing this many reads.
samplerate: Subsample reads to this fraction (0.0 to 1.0).
bamscript: Write a shell script to this path for SAM to BAM conversion.
scafstats: Write statistics on coverage of each reference scaffold.
covstats: Write coverage statistics to a file.
fast: Use faster, less sensitive presets.
slow: Use slower, more sensitive presets.
vslow: Use very slow, very sensitive presets.
max_indel: Do not look for indels longer than this.
min_identity: Approximate minimum identity of reads to map (0.0 to 1.0).
min_hits: Minimum number of seed hits required for candidate sites.
local_alignment: Use local instead of global alignments.
perfect_mode: Allow only perfect mappings.
ambiguous_reads_mode: Behavior for ambiguously-mapped reads ('best', 'all', 'random', 'toss').
sam_version: Set SAM version ('1.4' or '1.5').
secondary_alignments: Allow secondary alignments for ambiguous reads.
max_sites: Maximum number of sites to record per read.
pairlen: Maximum insert size for paired-end reads.
qtrim: Quality trimming mode ('l', 'r', 'lr', 'f' for left, right, both, or none).
untrim: Untrim reads.
trimq: Quality threshold for trimming.
min_avg_quality: Reads with average quality below this will be discarded.
nodisk: If True, do not write temporary files to disk.
Returns:
A dictionary containing the executed command, stdout, stderr, and a list of output files.
"""
# --- Input Validation ---
if not in_file.exists():
raise FileNotFoundError(f"Input file not found: {in_file}")
if not ref_file.exists():
raise FileNotFoundError(f"Reference file not found: {ref_file}")
if in2_file and not in2_file.exists():
raise FileNotFoundError(f"Second input file not found: {in2_file}")
if not (0.0 <= samplerate <= 1.0):
raise ValueError("samplerate must be between 0.0 and 1.0")
if not (0.0 <= min_identity <= 1.0):
raise ValueError("min_identity must be between 0.0 and 1.0")
valid_ambiguous_modes = {"best", "all", "random", "toss"}
if ambiguous_reads_mode not in valid_ambiguous_modes:
raise ValueError(f"ambiguous_reads_mode must be one of {valid_ambiguous_modes}")
valid_sam_versions = {"1.4", "1.5"}
if sam_version not in valid_sam_versions:
raise ValueError(f"sam_version must be one of {valid_sam_versions}")
valid_qtrim_modes = {"l", "r", "lr", "f"}
if qtrim not in valid_qtrim_modes:
raise ValueError(f"qtrim must be one of {valid_qtrim_modes}")
# --- Command Construction ---
cmd = ["bbmap.sh"]
if java_memory:
cmd.append(f"-Xmx{java_memory}")
# Required parameters
cmd.append(f"in={in_file}")
cmd.append(f"ref={ref_file}")
cmd.append(f"out={out_file}")
# Optional file paths
if in2_file:
cmd.append(f"in2={in2_file}")
if out_unmapped:
cmd.append(f"outu={out_unmapped}")
if bamscript:
cmd.append(f"bamscript={bamscript}")
if scafstats:
cmd.append(f"scafstats={scafstats}")
if covstats:
cmd.append(f"covstats={covstats}")
# Boolean flags (converted to 't'/'f')
if overwrite:
cmd.append("ow=t")
if fast:
cmd.append("fast=t")
if slow:
cmd.append("slow=t")
if vslow:
cmd.append("vslow=t")
if local_alignment:
cmd.append("local=t")
if perfect_mode:
cmd.append("perfectmode=t")
if secondary_alignments:
cmd.append("secondary=t")
if untrim:
cmd.append("untrim=t")
if nodisk:
cmd.append("nodisk=t")
# String and numeric parameters
if threads is not None:
cmd.append(f"threads={threads}")
if interleaved != "auto":
cmd.append(f"interleaved={interleaved}")
if reads != -1:
cmd.append(f"reads={reads}")
if samplerate != 1.0:
cmd.append(f"samplerate={samplerate}")
if max_indel != 16000:
cmd.append(f"maxindel={max_indel}")
if min_identity != 0.76:
cmd.append(f"minid={min_identity}")
if min_hits != 1:
cmd.append(f"minhits={min_hits}")
if ambiguous_reads_mode != "best":
cmd.append(f"ambiguous={ambiguous_reads_mode}")
if sam_version != "1.4":
cmd.append(f"sam={sam_version}")
if max_sites != 5:
cmd.append(f"maxsites={max_sites}")
if pairlen != 32000:
cmd.append(f"pairlen={pairlen}")
if qtrim != "f":
cmd.append(f"qtrim={qtrim}")
if trimq != 6:
cmd.append(f"trimq={trimq}")
if min_avg_quality != 0:
cmd.append(f"maq={min_avg_quality}")
# --- Subprocess Execution ---
command_str = " ".join(cmd)
try:
result = subprocess.run(
cmd,
capture_output=True,
text=True,
check=True,
)
except FileNotFoundError:
return {
"error": "bbmap.sh not found. Please ensure BBMap is in your PATH.",
"command_executed": command_str,
"stdout": "",
"stderr": "Executable not found.",
}
except subprocess.CalledProcessError as e:
return {
"error": "BBMap execution failed.",
"command_executed": command_str,
"stdout": e.stdout,
"stderr": e.stderr,
"return_code": e.returncode,
}
# --- Collect Output Files ---
output_files = [str(out_file)]
if out_unmapped:
output_files.append(str(out_unmapped))
if bamscript:
output_files.append(str(bamscript))
if scafstats:
output_files.append(str(scafstats))
if covstats:
output_files.append(str(covstats))
return {
"command_executed": command_str,
"stdout": result.stdout,
"stderr": result.stderr,
"output_files": output_files,
} |