File size: 5,316 Bytes
944e4a0 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 | #!/usr/bin/env python3
"""
Scan pieces/2026_01_26 for cullpdb_* list and .fasta pairs. Writes:
1) cullpdb_list_fasta_index.csv - paired only, with full paths
2) cullpdb_full_compiled_list.csv - every list and every fasta found (full compiled list)
"""
import csv
import re
from pathlib import Path
from typing import Optional
SCRIPT_DIR = Path(__file__).resolve().parent
BASE = SCRIPT_DIR.parent
CULLPDB_DIR = BASE / "pieces" / "2026_01_26"
CURATED_DIR = BASE / "curated_csv"
OUT_CSV = CURATED_DIR / "cullpdb_list_fasta_index.csv"
FULL_LIST_CSV = CURATED_DIR / "cullpdb_full_compiled_list.csv"
# cullpdb_pc20.0_res0.0-1.0_noBrks_len40-10000_R0.2_Xray_d2026_01_26_chains300
PAT = re.compile(
r"^cullpdb_pc([\d.]+)_res([\d.]+)-([\d.]+)_"
r"(?:(noBrks)_)?"
r"len40-10000_R([\d.]+)_"
r"(.+?)_d\d{4}_\d{2}_\d{2}_chains(\d+)$"
)
def parse_basename(name: str) -> Optional[dict]:
base = name.removesuffix(".fasta")
m = PAT.match(base)
if not m:
return None
pc, res_min, res_max, no_brks, r_cutoff, methods, n_chains = m.groups()
n = int(n_chains)
no_brk = no_brks is not None
return {
"list_basename": base,
"fasta_basename": base + ".fasta",
"n_chains": n,
"pc": float(pc),
"resolution": f"{res_min}-{res_max}",
"no_breaks": "yes" if no_brk else "no",
"R": float(r_cutoff),
"Nmethods": methods,
}
def main():
dir_path = Path(CULLPDB_DIR)
if not dir_path.is_dir():
print(f"Missing cullpdb dir: {dir_path}")
return
dir_path = dir_path.resolve()
# Collect every basename that has a list and/or fasta
bases = set()
for p in dir_path.iterdir():
if not p.is_file():
continue
name = p.name
if not name.startswith("cullpdb_") or "len40-10000" not in name:
continue
base = name.removesuffix(".fasta")
bases.add(base)
# Full compiled list: one row per basename, list path + fasta path (full), and parsed params
full_rows = []
paired_rows = []
for base in sorted(bases):
list_path = dir_path / base
fasta_path = dir_path / (base + ".fasta")
list_exists = list_path.exists()
fasta_exists = fasta_path.exists()
parsed = parse_basename(base)
if not parsed:
full_rows.append({
"list_basename": base,
"fasta_basename": base + ".fasta",
"list_path": str(list_path) if list_exists else "",
"fasta_path": str(fasta_path) if fasta_exists else "",
"list_exists": list_exists,
"fasta_exists": fasta_exists,
"paired": list_exists and fasta_exists,
"n_chains": "",
"pc": "",
"resolution": "",
"no_breaks": "",
"R": "",
"Nmethods": "",
})
continue
row_full = {
"list_basename": base,
"fasta_basename": base + ".fasta",
"list_path": str(list_path) if list_exists else "",
"fasta_path": str(fasta_path) if fasta_exists else "",
"list_exists": list_exists,
"fasta_exists": fasta_exists,
"paired": list_exists and fasta_exists,
"n_chains": parsed["n_chains"],
"pc": parsed["pc"],
"resolution": parsed["resolution"],
"no_breaks": parsed["no_breaks"],
"R": parsed["R"],
"Nmethods": parsed["Nmethods"],
}
full_rows.append(row_full)
if list_exists and fasta_exists:
paired_rows.append({
"list_basename": base,
"fasta_basename": base + ".fasta",
"list_path": str(list_path),
"fasta_path": str(fasta_path),
"n_chains": parsed["n_chains"],
"pc": parsed["pc"],
"resolution": parsed["resolution"],
"no_breaks": parsed["no_breaks"],
"R": parsed["R"],
"Nmethods": parsed["Nmethods"],
})
CURATED_DIR.mkdir(parents=True, exist_ok=True)
# 1) Paired index with full paths
fieldnames = [
"list_basename", "fasta_basename", "list_path", "fasta_path",
"n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
]
with open(OUT_CSV, "w", newline="") as f:
w = csv.DictWriter(f, fieldnames=fieldnames)
w.writeheader()
w.writerows(paired_rows)
print(f"Wrote {OUT_CSV} with {len(paired_rows)} list↔fasta pairs (full paths).")
# 2) Full compiled list: every basename, list/fasta paths and exists flags
full_fieldnames = [
"list_basename", "fasta_basename", "list_path", "fasta_path",
"list_exists", "fasta_exists", "paired",
"n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
]
with open(FULL_LIST_CSV, "w", newline="") as f:
w = csv.DictWriter(f, fieldnames=full_fieldnames)
w.writeheader()
w.writerows(full_rows)
n_paired = sum(1 for r in full_rows if r["paired"])
print(f"Wrote {FULL_LIST_CSV} with {len(full_rows)} entries (full compiled list); {n_paired} paired.")
if __name__ == "__main__":
main()
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