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完善真实样本的预测以及结果解读

This commit is contained in:
Chenlab 2025-06-12 02:52:35 +08:00
parent f320a1696f
commit 6f7510455a
5 changed files with 412 additions and 6 deletions
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6
FScanpy/data/__init__.py
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@ -22,6 +22,7 @@ def get_test_data_path(filename: str) -> str:
>>> blastx_file = get_test_data_path('blastx_example.xlsx') >>> blastx_file = get_test_data_path('blastx_example.xlsx')
>>> mrna_file = get_test_data_path('mrna_example.fasta') >>> mrna_file = get_test_data_path('mrna_example.fasta')
>>> region_file = get_test_data_path('region_example.csv') >>> region_file = get_test_data_path('region_example.csv')
>>> full_seq_file = get_test_data_path('full_seq.xlsx')
""" """
current_dir = Path(__file__).parent current_dir = Path(__file__).parent
test_data_dir = current_dir / "test_data" test_data_dir = current_dir / "test_data"
@ -93,7 +94,8 @@ def print_test_data_info():
file_descriptions = { file_descriptions = {
'blastx_example.xlsx': '🧬 BLASTX比对结果示例 (1000条记录)', 'blastx_example.xlsx': '🧬 BLASTX比对结果示例 (1000条记录)',
'mrna_example.fasta': '🧬 mRNA序列示例数据', 'mrna_example.fasta': '🧬 mRNA序列示例数据',
'region_example.csv': '🎯 PRF区域验证数据 (含标签)' 'region_example.csv': '🎯 PRF区域验证数据 (含标签)',
'full_seq.xlsx': '🧬 完整序列示例数据'
} }
for filename in files: for filename in files:
@ -112,7 +114,7 @@ def print_test_data_info():
print(" blastx_file = get_test_data_path('blastx_example.xlsx')") print(" blastx_file = get_test_data_path('blastx_example.xlsx')")
print(" mrna_file = get_test_data_path('mrna_example.fasta')") print(" mrna_file = get_test_data_path('mrna_example.fasta')")
print(" region_file = get_test_data_path('region_example.csv')") print(" region_file = get_test_data_path('region_example.csv')")
print(" full_seq_file = get_test_data_path('full_seq.xlsx')")
except Exception as e: except Exception as e:
print(f"❌ 获取数据信息时出错: {e}") print(f"❌ 获取数据信息时出错: {e}")

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FScanpy/data/test_data/full_seq.xlsx Normal file
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predict_sample.ipynb Normal file
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3
pyproject.toml
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@ -15,7 +15,8 @@ dependencies = [
"matplotlib>=3.9.4", "matplotlib>=3.9.4",
"joblib>=1.4.2", "joblib>=1.4.2",
"biopython>=1.85", "biopython>=1.85",
"wrapt>=1.17.0" "wrapt>=1.17.0",
"openpyxl>=3.1.5"
] ]
requires-python = ">=3.9" requires-python = ">=3.9"

7
tutorial/tutorial.md
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@ -369,6 +369,7 @@ list_test_data()
blastx_file = get_test_data_path('blastx_example.xlsx') blastx_file = get_test_data_path('blastx_example.xlsx')
mrna_file = get_test_data_path('mrna_example.fasta') mrna_file = get_test_data_path('mrna_example.fasta')
region_file = get_test_data_path('region_example.csv') region_file = get_test_data_path('region_example.csv')
seq_file = get_test_data_path('full_seq.xlsx')
``` ```
## Complete Workflow Examples ## Complete Workflow Examples
@ -380,15 +381,15 @@ from FScanpy import predict_prf, plot_prf_prediction
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
# Define sequence # Define sequence
sequence = "ATGCGTACGTATGCGTACGTATGCGTACGTAAGCCCTTTGAACCCAAAGGG" full_seq = pd.read.excel(seq_file)
# Method 1: Simple prediction # Method 1: Simple prediction
results = predict_prf(sequence=sequence) results = predict_prf(sequence=full_seq[0]['full_seq'])
print(f"Found {len(results)} potential sites") print(f"Found {len(results)} potential sites")
# Method 2: Prediction with visualization # Method 2: Prediction with visualization
results, fig = plot_prf_prediction( results, fig = plot_prf_prediction(
sequence=sequence, sequence=sequence=full_seq[0]['full_seq'],
window_size=1, # Scan every position window_size=1, # Scan every position
short_threshold=0.3, # Display sites above 0.3 short_threshold=0.3, # Display sites above 0.3
long_threshold=0.4, # Display sites above 0.4 long_threshold=0.4, # Display sites above 0.4