shuaizhou

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shuaizhou / gistfile1.txt

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1 https://www.researching.cn/ArticlePdf/m60022/2026/11/1/TFSR-2023-0188.pdf
2
3 https://www.biorxiv.org/content/10.1101/2021.06.25.449870v1.full

shuaizhou / multinomial_logistic.2.py

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1 import io
2 from typing import List, Tuple
3
4 import numpy as np
5 import pandas as pd
6 from sklearn.linear_model import LinearRegression
7
8
9 def fit_exact_webtool_softmax(
10 x: pd.DataFrame, y: pd.DataFrame

shuaizhou / multinomial_logistic.1.py

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1 import numpy as np
2 import pandas as pd
3
4 def build_design_matrix(x: pd.DataFrame) -> np.ndarray:
5 """
6 在最前面加一列 1 作为截距项
7 """
8 X = x.to_numpy(dtype=float)
9 intercept = np.ones((X.shape[0], 1), dtype=float)
10 return np.hstack([intercept, X])

shuaizhou / parser_vcf.py

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1 import os
2 import re
3 import gzip
4 from typing import Tuple, List
5 import pandas as pd
6
7 class QC:
8 _DP_RE = re.compile(r"(?:^|;)\s*DP=(\d+(?:\.\d+)?)")
9
10 def __init__(

shuaizhou / coefficiet.sh

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1 # help
2 docker run --rm -u 1008:1008 -it -v /data01/lihaicheng:/data01/lihaicheng coefficient:dev
3
4 # demo
5 docker run --rm -u 1008:1008 -it -v /data01/lihaicheng:/data01/lihaicheng coefficient:dev --sample 1,2 --vcf /data01/lihaicheng/project148/sz01-task-geneseek-20251219359395960000005/result/test-geneseek-1/test-geneseek-1.filter.vcf.gz,/data01/lihaicheng/project148/sz01-task-geneseek-20251219359395960000005/result/test-geneseek-2/test-geneseek-2.filter.vcf.gz --output /data01/lihaicheng/project157/result

shuaizhou / ncbi_genome_download.sh

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1 conda create -n ncbi_dl -y -c conda-forge ncbi-datasets-cli jq
2
3 for f in batches/batch_*; do
4 base=$(basename "$f")
5 out="zips/${base}.zip"
6
7 echo "Downloading $f -> $out"
8 datasets download genome accession --inputfile "$f" \
9 --include genome,gff3,gbff \
10 --filename "$out"
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