wehub-resource-sync
70 lines
1.7 KiB
Python
70 lines
1.7 KiB
Python
"""
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Utility modules for nf-core pipeline deployment.
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Modules:
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ncbi_utils: NCBI/GEO/SRA data fetching and download utilities
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file_discovery: Find FASTQ, BAM, and CRAM files
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sample_inference: Extract sample info, detect tumor/normal
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validators: Validate samplesheets before writing
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"""
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# NCBI utilities for GEO/SRA data acquisition
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from .ncbi_utils import (
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check_network_access,
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fetch_geo_metadata,
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fetch_sra_study_accession,
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fetch_sra_run_info,
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fetch_sra_run_info_detailed,
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fetch_bioproject_from_geo,
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fetch_ena_fastq_urls,
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download_file,
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fetch_pubmed_metadata,
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format_file_size,
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estimate_download_size,
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group_samples_by_type,
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format_sample_groups_table,
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)
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# File discovery utilities
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from .file_discovery import discover_files, FileInfo, count_files_by_type
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# Sample inference utilities
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from .sample_inference import (
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extract_sample_info,
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infer_tumor_normal_status,
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match_read_pairs,
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extract_replicate_number
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)
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# Validation utilities
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from .validators import validate_samplesheet, ValidationResult
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__all__ = [
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# ncbi_utils
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'check_network_access',
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'fetch_geo_metadata',
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'fetch_sra_study_accession',
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'fetch_sra_run_info',
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'fetch_sra_run_info_detailed',
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'fetch_bioproject_from_geo',
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'fetch_ena_fastq_urls',
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'download_file',
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'fetch_pubmed_metadata',
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'format_file_size',
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'estimate_download_size',
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'group_samples_by_type',
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'format_sample_groups_table',
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# file_discovery
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'discover_files',
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'FileInfo',
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'count_files_by_type',
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# sample_inference
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'extract_sample_info',
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'infer_tumor_normal_status',
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'match_read_pairs',
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'extract_replicate_number',
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# validators
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'validate_samplesheet',
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'ValidationResult',
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]
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