Code implementation of integrated tools framework from documentation to automated pipelines

import re, json, time, random
from dataclasses import dataclass
from typing import Callable, Dict, Any, List, Tuple


@dataclass
class ToolSpec:
   name: str
   description: str
   inputs: Dict[str, str]
   outputs: Dict[str, str]


def parse_doc_to_spec(name: str, doc: str) -> ToolSpec:
   desc = doc.strip().splitlines()[0].strip() if doc.strip() else name
   arg_block = "n".join([l for l in doc.splitlines() if "--" in l or ":" in l])
   inputs = {}
   for line in arg_block.splitlines():
       m = re.findall(r"(--?w[w-]*|bw+b)s*[:=]?s*(w+)?", line)
       for key, typ in m:
           k = key.lstrip("-")
           if k and k not in inputs and k not in ["Returns","Output","Outputs"]:
               inputs[k] = (typ or "str")
   if not inputs: inputs = {"in": "str"}
   return ToolSpec(name=name, description=desc, inputs=inputs, outputs={"out":"json"})

def tool_fastqc(seq_fasta: str, min_len:int=30) -> Dict[str,Any]:
   seqs = [s for s in re.split(r">[^n]*n", seq_fasta)[1:]]
   lens = [len(re.sub(r"s+","",s)) for s in seqs]
   q30 = sum(l>=min_len for l in lens)/max(1,len(lens))
   gc = sum(c in "GCgc" for s in seqs for c in s)/max(1,sum(lens))
   return {"n_seqs":len(lens),"len_mean":(sum(lens)/max(1,len(lens))),"pct_q30":q30,"gc":gc}


def tool_bowtie2_like(ref:str, reads:str, mode:str="end-to-end") -> Dict[str,Any]:
   def revcomp(s):
       t=str.maketrans("ACGTacgt","TGCAtgca"); return s.translate
   reads_list=[r for r in re.split(r">[^n]*n", reads)[1:]]
   ref_seq="".join(ref.splitlines()[1:])
   hits=[]
   for i,r in enumerate(reads_list):
       rseq="".join(r.split())
       aligned = (rseq in ref_seq) or (revcomp(rseq) in ref_seq)
       hits.append({"read_id":i,"aligned":bool(aligned),"pos":ref_seq.find(rseq)})
   return {"n":len(hits),"aligned":sum(h["aligned"] for h in hits),"mode":mode,"hits":hits}


def tool_bcftools_like(ref:str, alt:str, win:int=15) -> Dict[str,Any]:
   ref_seq="".join(ref.splitlines()[1:]); alt_seq="".join(alt.splitlines()[1:])
   n=min(len(ref_seq),len(alt_seq)); vars=[]
   for i in range(n):
       if ref_seq[i]!=alt_seq[i]: vars.append({"pos":i,"ref":ref_seq[i],"alt":alt_seq[i]})
   return {"n_sites":n,"n_var":len(vars),"variants":vars[:win]}


FASTQC_DOC = """FastQC-like quality control for FASTA
--seq_fasta: str  --min_len: int   Outputs: json"""
BOWTIE_DOC = """Bowtie2-like aligner
--ref: str  --reads: str  --mode: str  Outputs: json"""
BCF_DOC = """bcftools-like variant caller
--ref: str  --alt: str  --win: int  Outputs: json"""

@dataclass
class MCPTool:
   spec: ToolSpec
   fn: Callable[..., Dict[str,Any]]


class MCPServer:
   def __init__(self): self.tools: Dict[str,MCPTool] = {}
   def register(self, name:str, doc:str, fn:Callable[...,Dict[str,Any]]):
       spec = parse_doc_to_spec(name, doc); self.tools[name]=MCPTool(spec, fn)
   def list_tools(self) -> List[Dict[str,Any]]:
       return [dict(name=t.spec.name, description=t.spec.description, inputs=t.spec.inputs, outputs=t.spec.outputs) for t in self.tools.values()]
   def call_tool(self, name:str, args:Dict[str,Any]) -> Dict[str,Any]:
       if name not in self.tools: raise KeyError(f"tool {name} not found")
       spec = self.tools[name].spec
       kwargs={k:args.get(k) for k in spec.inputs.keys()}
       return self.tools[name].fn(**kwargs)


server=MCPServer()
server.register("fastqc", FASTQC_DOC, tool_fastqc)
server.register("bowtie2", BOWTIE_DOC, tool_bowtie2_like)
server.register("bcftools", BCF_DOC, tool_bcftools_like)


Task = Tuple[str, Dict[str,Any]]
PIPELINES = {
   "rnaseq_qc_align_call":[
       ("fastqc", {"seq_fasta":"{reads}", "min_len":30}),
       ("bowtie2", {"ref":"{ref}", "reads":"{reads}", "mode":"end-to-end"}),
       ("bcftools", {"ref":"{ref}", "alt":"{alt}", "win":15}),
   ]
}


def compile_pipeline(nl_request:str) -> List[Task]:
   key = "rnaseq_qc_align_call" if re.search(r"rna|qc|align|variant|call", nl_request, re.I) else "rnaseq_qc_align_call"
   return PIPELINES[key]

def mk_fasta(header:str, seq:str)->str: return f">{header}n{seq}n"
random.seed(0)
REF_SEQ="".join(random.choice("ACGT") for _ in range(300))
REF = mk_fasta("ref",REF_SEQ)
READS = mk_fasta("r1", REF_SEQ[50:130]) + mk_fasta("r2","ACGT"*15) + mk_fasta("r3", REF_SEQ[180:240])
ALT = mk_fasta("alt", REF_SEQ[:150] + "T" + REF_SEQ[151:])


def run_pipeline(nl:str, ctx:Dict[str,str]) -> Dict[str,Any]:
   plan=compile_pipeline(nl); results=[]; t0=time.time()
   for name, arg_tpl in plan:
       args={k:(v.format(**ctx) if isinstance(v,str) else v) for k,v in arg_tpl.items()}
       out=server.call_tool(name, args)
       results.append({"tool":name,"args":args,"output":out})
   return {"request":nl,"elapsed_s":round(time.time()-t0,4),"results":results}

def bench_individual() -> List[Dict[str,Any]]:
   cases=[
       ("fastqc", {"seq_fasta":READS,"min_len":25}),
       ("bowtie2", {"ref":REF,"reads":READS,"mode":"end-to-end"}),
       ("bcftools", {"ref":REF,"alt":ALT,"win":10}),
   ]
   rows=[]
   for name,args in cases:
       t0=time.time(); ok=True; err=None; out=None
       try: out=server.call_tool(name,args)
       except Exception as e: ok=False; err=str(e)
       rows.append({"tool":name,"ok":ok,"ms":int((time.time()-t0)*1000),"out_keys":list(out.keys()) if ok else [],"err":err})
   return rows


def bench_pipeline() -> Dict[str,Any]:
   t0=time.time()
   res=run_pipeline("Run RNA-seq QC, align, and variant call.", {"ref":REF,"reads":READS,"alt":ALT})
   ok = all(step["output"] for step in res["results"])
   return {"pipeline":"rnaseq_qc_align_call","ok":ok,"ms":int((time.time()-t0)*1000),"n_steps":len(res["results"])}


print("== TOOLS =="); print(json.dumps(server.list_tools(), indent=2))
print("n== INDIVIDUAL BENCH =="); print(json.dumps(bench_individual(), indent=2))
print("n== PIPELINE BENCH =="); print(json.dumps(bench_pipeline(), indent=2))
print("n== PIPELINE RUN =="); print(json.dumps(run_pipeline("Run RNA-seq QC, align, and variant call.", {"ref":REF,"reads":READS,"alt":ALT}), indent=2))