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import tempfile
from pathlib import Path
from typing import List, Optional
# MCP decorator is commented out as per instructions
# import mcp
from mcp.server.fastmcp import FastMCP
SERVER_NAME = 'local_bedops'
mcp = FastMCP(SERVER_NAME)
@mcp.tool()
def bedops_complement(
files: List[Path],
chop_to_limits: bool = False,
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Computes the complement of one or more BED files.
This corresponds to the `bedops -c` or `bedops --complement` operation.
It finds the regions within chromosome boundaries that are not covered by
any intervals in the input file(s).
Args:
files: A list of one or more input BED/Starch files. Must be sorted.
chop_to_limits: If True, chop complementary regions to chromosome limits
defined by the first input file (-L flag).
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if not files:
raise ValueError("At least one input file must be provided for the complement operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--complement")
if chop_to_limits:
cmd.append("-L")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops complement failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_difference(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Computes the difference between a reference BED file and one or more other BED files.
This corresponds to the `bedops -d` or `bedops --difference` operation.
It returns regions from the first (reference) file that do not overlap
with any regions in the subsequent files.
Args:
files: A list of two or more input BED/Starch files. The first file is
the reference. All files must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if len(files) < 2:
raise ValueError("At least two input files (a reference and one other) must be provided for the difference operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--difference")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops difference failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_element_of(
files: List[Path],
overlap_criterion: str = "100%",
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Finds elements in the reference file that overlap other files by a specified amount.
This corresponds to the `bedops -e` or `bedops --element-of` operation.
It returns elements from the first (reference) file that overlap elements
in any of the other files by at least the specified amount.
Args:
files: A list of two or more input BED/Starch files. The first file is
the reference. All files must be sorted.
overlap_criterion: The required overlap, as base pairs (e.g., '1') or
percentage (e.g., '50%'). Defaults to '100%'.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' or 'S' format. The first (reference)
file is NOT padded with this operation.
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if len(files) < 2:
raise ValueError("At least two input files (a reference and one other) must be provided for the element-of operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.extend(["--element-of", overlap_criterion])
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops element-of failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_intersect(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Computes the intersection of two or more BED files.
This corresponds to the `bedops -i` or `bedops --intersect` operation.
It returns regions that are common to all input files.
Args:
files: A list of two or more input BED/Starch files. All files must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if len(files) < 2:
raise ValueError("At least two input files must be provided for the intersect operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--intersect")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops intersect failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_merge(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Merges overlapping regions from one or more BED files.
This corresponds to the `bedops -m` or `bedops --merge` operation.
It combines overlapping or adjacent intervals into a single, larger interval.
Args:
files: A list of one or more input BED/Starch files. Must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if not files:
raise ValueError("At least one input file must be provided for the merge operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--merge")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops merge failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_not_element_of(
files: List[Path],
overlap_criterion: str = "100%",
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Finds elements in the reference file that DO NOT overlap other files by a specified amount.
This corresponds to the `bedops -n` or `bedops --not-element-of` operation.
It is the inverse of the `element-of` operation.
Args:
files: A list of two or more input BED/Starch files. The first file is
the reference. All files must be sorted.
overlap_criterion: The required overlap, as base pairs (e.g., '1') or
percentage (e.g., '50%'). Defaults to '100%'.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' or 'S' format. The first (reference)
file is NOT padded with this operation.
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if len(files) < 2:
raise ValueError("At least two input files (a reference and one other) must be provided for the not-element-of operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.extend(["--not-element-of", overlap_criterion])
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops not-element-of failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_partition(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Partitions the input BED file(s) into disjoint segments.
This corresponds to the `bedops -p` or `bedops --partition` operation.
It breaks the input regions into non-overlapping segments, reporting each
new segment and which input files it came from.
Args:
files: A list of one or more input BED/Starch files. Must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if not files:
raise ValueError("At least one input file must be provided for the partition operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--partition")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops partition failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_symmdiff(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Computes the symmetric difference of two or more BED files.
This corresponds to the `bedops -s` or `bedops --symmdiff` operation.
It returns regions that are unique to any of the input files (i.e., not
present in their intersection).
Args:
files: A list of two or more input BED/Starch files. All files must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if len(files) < 2:
raise ValueError("At least two input files must be provided for the symmetric difference operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--symmdiff")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops symmdiff failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_everything(
files: List[Path],
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Returns the union of all elements from input files without merging.
This corresponds to the `bedops -u` or `bedops --everything` operation.
It effectively concatenates the input files while maintaining sort order
and preserving all original columns.
Args:
files: A list of one or more input BED/Starch files. Must be sorted.
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if not files:
raise ValueError("At least one input file must be provided for the everything operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.append("--everything")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops everything failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
@mcp.tool()
def bedops_chop(
files: List[Path],
bp: int = 1,
stagger: Optional[int] = None,
exclusive_chop: bool = False,
chrom: Optional[str] = None,
ec: bool = False,
header: bool = False,
range_str: Optional[str] = None,
output_file: Optional[Path] = None,
) -> dict:
"""
Chops elements into fixed-size, potentially staggered sub-elements.
This corresponds to the `bedops -w` or `bedops --chop` operation.
Args:
files: A list of one or more input BED/Starch files. Must be sorted.
bp: The size in base pairs of each chopped element. Defaults to 1.
stagger: The stagger distance in nucleotides. If not set, no staggering is done.
exclusive_chop: If True, removes single-base elements that can result
from chopping (-x flag).
chrom: Process data for the given chromosome only.
ec: Error check input files (slower).
header: Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
range_str: Pad coordinates. Use 'L:R' format (e.g., '-10:20') or a
single value 'S' for symmetric padding (e.g., '100').
output_file: Optional path to save the output. If not provided,
output is returned as a string in the result dictionary.
Returns:
A dictionary containing the command executed, stdout, stderr, and a
list of output files generated.
"""
if not files:
raise ValueError("At least one input file must be provided for the chop operation.")
for file_path in files:
if not file_path.exists():
raise FileNotFoundError(f"Input file not found: {file_path}")
cmd = ["bedops"]
if chrom:
cmd.extend(["--chrom", chrom])
if ec:
cmd.append("--ec")
if header:
cmd.append("--header")
if range_str:
cmd.extend(["--range", range_str])
cmd.extend(["--chop", str(bp)])
if stagger is not None:
cmd.extend(["--stagger", str(stagger)])
if exclusive_chop:
cmd.append("-x")
cmd.extend([str(p) for p in files])
try:
if output_file:
with open(output_file, "w") as f:
result = subprocess.run(
cmd, check=True, text=True, stdout=f, stderr=subprocess.PIPE
)
stdout_capture = ""
output_files_list = [str(output_file)]
else:
result = subprocess.run(
cmd, check=True, text=True, capture_output=True
)
stdout_capture = result.stdout
output_files_list = []
return {
"command_executed": " ".join(cmd),
"stdout": stdout_capture,
"stderr": result.stderr,
"output_files": output_files_list,
}
except subprocess.CalledProcessError as e:
raise RuntimeError(
f"bedops chop failed with exit code {e.returncode}\n"
f"Stderr: {e.stderr}\n"
f"Stdout: {e.stdout}\n"
f"Command: {' '.join(cmd)}"
) from e
if __name__ == "__main__":
mcp.run(transport="stdio")
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