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Remove Custom Field Selection and Population-Specific Exports sections
- Remove detailed custom TSV field configuration section - Remove population-based export workflow section - Simplify export guide to focus on core functionality
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@@ -62,72 +62,6 @@ ds.export_tsv(
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)
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```
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### Custom Field Selection
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```python
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# Define custom TSV fields
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custom_fields = [
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"CHR", # Chromosome
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"POS", # Position
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"ID", # Variant ID
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"REF", # Reference allele
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"ALT", # Alternative allele
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"QUAL", # Quality score
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"FILTER", # Filter status
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"I:AF", # INFO: Allele frequency
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"I:AC", # INFO: Allele count
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"I:AN", # INFO: Allele number
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"S:GT", # Sample: Genotype
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"S:DP", # Sample: Depth
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"S:GQ" # Sample: Genotype quality
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]
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ds.export_tsv(
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uri="detailed_variants.tsv",
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regions=["chr1:1000000-2000000"],
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samples=["SAMPLE_001", "SAMPLE_002"],
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tsv_fields=custom_fields
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)
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```
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### Population-Specific Exports
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```python
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def export_population_data(ds, regions, population_file, output_prefix):
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"""Export data for different populations separately"""
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import pandas as pd
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# Read population assignments
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pop_df = pd.read_csv(population_file)
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populations = {}
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for _, row in pop_df.iterrows():
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pop = row['population']
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if pop not in populations:
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populations[pop] = []
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populations[pop].append(row['sample_id'])
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# Export each population
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for pop_name, samples in populations.items():
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output_file = f"{output_prefix}_{pop_name}.tsv"
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print(f"Exporting {pop_name}: {len(samples)} samples")
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ds.export_tsv(
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uri=output_file,
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regions=regions,
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samples=samples,
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tsv_fields=["CHR", "POS", "REF", "ALT", "S:GT", "S:AF"]
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)
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print(f"Exported {pop_name} data to {output_file}")
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# Usage
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export_population_data(
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ds,
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regions=["chr1:1000000-2000000"],
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population_file="populations.csv",
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output_prefix="population_variants"
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)
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```
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## Pandas DataFrame Export
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