File size: 3,979 Bytes
50dd82b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 | """Parse InterPro flat files into a queryable cache.
Downloads from:
- https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
- https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/ParentChildTreeFile.txt
Produces:
- tmp/mcq_build/interpro_cache.json
{
"entries": {"IPR000169": {"type": "Active_site",
"name": "Cysteine peptidase, active site"}},
"parent": {"IPR037302": "IPR000008", ...}, # child -> parent
"children": {"IPR000008": ["IPR014705", ...]}, # parent -> children
"roots": ["IPR000008", ...], # entries with no parent (hierarchy roots)
}
Parent-child tree file format:
IPR000008::C2 domain::
--IPR014705::Synaptotagmin-17, C2B domain::
----IPR037302::deeper nesting::
Indentation level = 2 * depth (each "--" pair adds one level).
"""
from __future__ import annotations
import json
import re
from pathlib import Path
HERE = Path(__file__).parent
ENTRY_LIST = HERE / "entry.list"
TREE_FILE = HERE / "ParentChildTreeFile.txt"
OUTPUT = HERE / "interpro_cache.json"
IPR_LINE_RE = re.compile(r"^(-*)(IPR\d{6})::([^:]*)::")
def parse_entries() -> dict[str, dict[str, str]]:
"""Parse entry.list → {IPR: {type, name}}."""
entries: dict[str, dict[str, str]] = {}
with open(ENTRY_LIST) as f:
header = f.readline()
assert header.startswith("ENTRY_AC"), f"unexpected header: {header!r}"
for line in f:
parts = line.rstrip("\n").split("\t")
if len(parts) < 3:
continue
ac, etype, name = parts[0], parts[1], parts[2]
if not ac.startswith("IPR"):
continue
entries[ac] = {"type": etype, "name": name}
return entries
def parse_tree() -> tuple[dict[str, str], dict[str, list[str]], list[str]]:
"""Parse ParentChildTreeFile.txt → (parent_map, children_map, roots).
Returns:
parent: dict mapping child IPR → immediate parent IPR
children: dict mapping parent IPR → list of immediate child IPRs
roots: list of IPRs that appear as top-level entries (depth 0)
"""
parent: dict[str, str] = {}
children: dict[str, list[str]] = {}
roots: list[str] = []
# Stack of (depth, IPR) for current lineage
stack: list[tuple[int, str]] = []
with open(TREE_FILE) as f:
for raw in f:
line = raw.rstrip("\n")
if not line:
continue
m = IPR_LINE_RE.match(line)
if not m:
continue
dashes, ac, _name = m.group(1), m.group(2), m.group(3)
depth = len(dashes) // 2
# Pop stack until we find the parent depth
while stack and stack[-1][0] >= depth:
stack.pop()
if stack:
par = stack[-1][1]
parent[ac] = par
children.setdefault(par, []).append(ac)
else:
roots.append(ac)
children.setdefault(ac, [])
stack.append((depth, ac))
return parent, children, roots
def main() -> int:
entries = parse_entries()
parent, children, roots = parse_tree()
cache = {
"entries": entries,
"parent": parent,
"children": children,
"roots": roots,
"stats": {
"n_entries": len(entries),
"n_in_hierarchy": len(parent) + len(roots),
"n_with_children": sum(1 for v in children.values() if v),
"n_roots": len(roots),
},
}
with open(OUTPUT, "w") as f:
json.dump(cache, f)
print(f"Saved {OUTPUT}")
print(f" entries: {cache['stats']['n_entries']}")
print(f" hierarchy nodes: {cache['stats']['n_in_hierarchy']}")
print(f" roots: {cache['stats']['n_roots']}")
print(f" entries with children: {cache['stats']['n_with_children']}")
return 0
if __name__ == "__main__":
raise SystemExit(main())
|