File size: 2,656 Bytes
0784fd3 | 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 | """Step 2: split the regex-filtered documents by how long their longest DNA sequence is.
Every DNA "word" in a document is found with tag_dna_sequences: a whitespace-delimited token of at least 6 letters that
is pure A/C/G/T, or IUPAC codes (12+ letters, at most 20% ambiguous), with surrounding punctuation and 5'/3' markers
stripped. A document whose longest DNA word is at least 39 bp, the 90th percentile of that length across the regex
data, goes to p90; everything else goes to rest. Short DNA words are mostly primers and motifs; p90 documents carry
real sequences.
python 2_p90_split.py --input ./dna_regex/fineweb_edu --p90 ./p90/fineweb_edu --rest ./rest/fineweb_edu
Input and output are jsonl.gz files with a "text" field, as written by step 1. One output file per input file.
"""
import argparse
import glob
import gzip
import json
import os
from tag_dna_sequences import tag_dna_sequences
P90_THRESHOLD = 39 # bp: the 90th percentile of the longest DNA word per document
MIN_LEN = 6 # bp: shortest token counted as DNA
def longest_dna(text: str) -> int:
_, _, seqs = tag_dna_sequences(text, min_len=MIN_LEN)
return max((len(s) for s in seqs), default=0)
def main():
ap = argparse.ArgumentParser(description="Split DNA-bearing documents into p90 (longest DNA >= 39 bp) and rest.")
ap.add_argument("--input", required=True, help="folder of jsonl.gz files from step 1")
ap.add_argument("--p90", required=True, help="output folder for p90 documents")
ap.add_argument("--rest", required=True, help="output folder for the rest")
ap.add_argument("--threshold", type=int, default=P90_THRESHOLD)
a = ap.parse_args()
os.makedirs(a.p90, exist_ok=True)
os.makedirs(a.rest, exist_ok=True)
n_p90 = n_rest = 0
for path in sorted(glob.glob(os.path.join(a.input, "**", "*.jsonl.gz"), recursive=True)):
name = os.path.basename(path)
with gzip.open(path, "rt", encoding="utf-8") as fin, \
gzip.open(os.path.join(a.p90, name), "wt", encoding="utf-8") as fp90, \
gzip.open(os.path.join(a.rest, name), "wt", encoding="utf-8") as frest:
for line in fin:
if not line.strip():
continue
text = json.loads(line).get("text") or ""
if longest_dna(text) >= a.threshold:
fp90.write(line if line.endswith("\n") else line + "\n"); n_p90 += 1
else:
frest.write(line if line.endswith("\n") else line + "\n"); n_rest += 1
print(f"p90: {n_p90:,} documents rest: {n_rest:,} documents")
if __name__ == "__main__":
main()
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