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dingyifei
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Feb 17, 2026
dingyifei
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- remove selenium, use NCBI dataset API for N50
- add method to query brc by taxon id (for 1a)
- Replace brc FTP downloads with HTTPS downloads
get_scaffold_n50_for_species() used Selenium + Chrome to scrape NCBI web pages, which fails in headless environments (WSL, CI). Replace with a direct call to the NCBI Datasets v2 REST API endpoint: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{id}/dataset_report Remove now-unused selenium, webdriver-manager, and beautifulsoup4 dependencies. Update test fixture to use exact API value (4641652) instead of rounded Selenium scrape (4600000). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add a function to query the BV-BRC Data API for genome records by taxon ID. Uses taxon_lineage_ids (not taxon_id) to include subspecies and strain-level descendants. Supports optional filtering by genome_status and genome_quality, with automatic pagination. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
BV-BRC's FTP server now requires SSL/TLS on the control channel, causing all genome downloads via urllib FTP to fail silently. Switch download_genomes_bvbrc() to use HTTPS Data API endpoints with proper content-type negotiation. Also fix stale loop variable bug in the bad_genomes cleanup code (was using `genome` instead of `bad_genome`). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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