"""
Utility functions for infercnv-mcp server.
"""
from fastmcp import FastMCP, Context
from fastmcp.exceptions import ToolError
from pathlib import Path
import os
from ...schema.preset.util import *
from scmcp_shared.util import add_op_log, savefig, filter_args, forward_request, get_ads
from scmcp_shared.logging_config import setup_logger
from scmcp_shared.schema import AdataInfo
import pandas as pd
from scmcp_shared.server.preset.util import ScanpyUtilMCP
ul_mcp = ScanpyUtilMCP(
include_tools=["check_samples"],
).mcp
@ul_mcp.tool()
def load_gene_position(
request: GenePosParam,
adinfo: AdataInfo = AdataInfo()
):
"""Load gene position file and add to adata.var when finished reading adata."""
logger = setup_logger()
try:
result = forward_request("load_gene_position", request, adinfo)
if result is not None:
return result
adata = get_ads().get_adata(adinfo=adinfo)
# Read gene position file
gene_pos = pd.read_csv(request.file, sep=request.sep, index_col=0)
# Validate required columns
required_cols = ['chromosome', 'start', 'end']
if not all(col in gene_pos.columns for col in required_cols):
msg = f"Gene position file must contain columns: {required_cols}"
raise ToolError(msg)
# Check if all genes in adata.var_names exist in gene_pos
missing_genes = set(adata.var_names) - set(gene_pos.index)
msg_ls = []
if missing_genes:
msg1 = f"Some genes in adata.var_names are missing from gene position file: {missing_genes[:10]}..."
msg_ls.append(msg1)
# Check if all genes in gene_pos exist in adata.var_names
extra_genes = set(gene_pos.index) - set(adata.var_names)
if extra_genes:
msg2 = f"Some genes in gene position file are not in adata.var_names: {extra_genes[:10]}..."
msg_ls.append(msg2)
# Add chromosome position information to adata.var
for col in ['chromosome', 'start', 'end']:
# Only add information for genes that exist in both adata.var_names and gene_pos
common_genes = list(set(adata.var_names) & set(gene_pos.index))
adata.var.loc[common_genes, col] = gene_pos.loc[common_genes, col]
return {
"msg": f"Gene position file loaded successfully.",
"notice": msg_ls
}
except ToolError as e:
raise ToolError(e)
except Exception as e:
raise ToolError(e)
