Blame for scripts/compare_ss_tools.py

"""Rebuild TAPE's CASP12 secondary-structure labels from the PDB with several tools and compare residue by residue.

usage: python -I scripts/compare_ss_tools.py [mkdssp-binary ...]
Reference: data/original/tape/secondary_structure/secondary_structure/secondary_structure_casp12.json (TAPE's download; ss8 ints decoded as G H I B E S T C).
Compared on residues TAPE marks as resolved (disorder == 1).
"""
import sys, json, collections
sys.path.insert(0, "scripts")
import ss_assign as A
from Bio import Align

S8, S3 = "GHIBESTC", "HEC"
tape = json.load(open("data/original/tape/secondary_structure/secondary_structure/secondary_structure_casp12.json"))
binaries = sys.argv[1:]

aligner = Align.PairwiseAligner(mode="global", match_score=2, mismatch_score=-1, open_gap_score=-5, extend_gap_score=-0.5)


def project(ref_seq, seqres, labels):
    """Map labels on `seqres` onto positions of `ref_seq` (identity if equal, else via global alignment)."""
    if ref_seq == seqres:
        return labels, "identical"
    aln = aligner.align(ref_seq, seqres)[0]
    out = [None] * len(ref_seq)
    for (a0, a1), (b0, b1) in zip(*aln.aligned):
        for k in range(a1 - a0):
            out[a0 + k] = labels[b0 + k]
    return out, f"aligned ({sum(a1 - a0 for (a0, a1), _ in zip(*aln.aligned))}/{len(ref_seq)} positions)"


tools = {"mdtraj (chain)": lambda st, ch: A.mdtraj_assign(st, ch, "chain"),
         "mdtraj (whole ASU)": lambda st, ch: A.mdtraj_assign(st, ch, "asu")}
try:
    import pydssp  # noqa: F401
    tools["PyDSSP (chain, 3-state)"] = lambda st, ch: A.pydssp_assign(st, ch)
except ImportError:
    print("PyDSSP not installed; skipping it")
for b in binaries:
    tools[f"{b} (chain)"] = lambda st, ch, b=b: A.mkdssp_assign(st, ch, b, "chain")
    tools[f"{b} (whole ASU)"] = lambda st, ch, b=b: A.mkdssp_assign(st, ch, b, "asu")

tot = {t: collections.Counter() for t in tools}
per_protein = collections.defaultdict(dict)
seq_notes, mask_notes = {}, {}
for rec in tape:
    pdb, ch = rec["id"].split("-")
    st = A.load(f"data/original/casp12_pdb/{pdb}.cif.gz")
    t8 = [S8[x] for x in rec["ss8"]]
    t3 = [S3[x] for x in rec["ss3"]]
    resolved = [d == 1 for d in rec["disorder"]]
    for name, fn in tools.items():
        seqres, labels = fn(st, ch)
        lab, how = project(rec["primary"], seqres, labels)
        seq_notes[rec["id"]] = how
        c = tot[name]
        p = collections.Counter()
        for i, ok in enumerate(resolved):
            have = lab[i] is not None
            if ok and not have:
                c["tape_resolved_tool_missing"] += 1
            if have and not ok:
                c["tool_has_tape_unresolved"] += 1
            if ok and have:
                if lab[i] == "P":  # DSSP 4 polyproline; older DSSP (and TAPE) call these residues coil
                    c["P_as_C"] += 1
                    lab[i] = "C"
                c["n"] += 1; p["n"] += 1
                l3 = A.SS8_TO_SS3.get(lab[i], lab[i])
                c["ss3"] += l3 == t3[i]; p["ss3"] += l3 == t3[i]
                if "PyDSSP" not in name:
                    c["ss8"] += lab[i] == t8[i]; p["ss8"] += lab[i] == t8[i]
                    if lab[i] != t8[i]:
                        c[f"conf {t8[i]}->{lab[i]}"] += 1
        per_protein[rec["id"]][name] = p
    print(rec["id"], seq_notes[rec["id"]], flush=True)

print("\n=== Agreement with TAPE CASP12 on TAPE-resolved residues")
for name, c in tot.items():
    n = c["n"]
    s8 = f"{100 * c['ss8'] / n:6.2f}%" if "PyDSSP" not in name else "   n/a "
    exact = sum(1 for pid in per_protein if per_protein[pid][name]["ss3"] == per_protein[pid][name]["n"])
    exact8 = sum(1 for pid in per_protein if per_protein[pid][name]["ss8"] == per_protein[pid][name]["n"]) if "PyDSSP" not in name else "-"
    print(f"{name:26s} residues={n:5d}  ss8={s8}  ss3={100 * c['ss3'] / n:6.2f}%  proteins identical ss3={exact}/21 ss8={exact8}/21"
          f"  | resolved-but-missing={c['tape_resolved_tool_missing']} tool-labels-on-unresolved={c['tool_has_tape_unresolved']}")
    conf = sorted(((k, v) for k, v in c.items() if k.startswith("conf ")), key=lambda kv: -kv[1])[:8]
    if conf:
        print("      top ss8 disagreements (TAPE->tool):", ", ".join(f"{k[5:]}:{v}" for k, v in conf))
print("\nPer protein ss8 agreement:", " / ".join(n for n in tools if "PyDSSP" not in n))
for pid, d in per_protein.items():
    print(f"  {pid:8s} n={d['mdtraj (chain)']['n']:4d}  " + "  ".join(f"{100 * d[n]['ss8'] / max(d[n]['n'], 1):6.2f}%" for n in tools if "PyDSSP" not in n))