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Utility script for bulk download of genomes from KBase usage: python3 download_narrative_genomes.py [-n NARRATIVE] [-t TOKEN] [-f FORMAT] Arguments: -n NARRATIVE Narrative identifier (for example, 49058 from https://narrative.kbase.us/narrative/49058). You must have an access to this narrative. -t TOKEN Authorization token from kbase_session or kbase_session_backup field of kbase.us cookies -f FORMAT File format. Acceptable values: gbk, gff, faa. Export to GenBank also generates nuclotide fasta files in "contigs" subdirectory Output depends on -f argument value gff: GFF files in gff subdirectory gbk: Genbank files in genbank subdirectory and nuclotide FASTA files in contigs subdirectory faa: Protein FASTA files in proteins subdirectory Script also creates text file with list of genome objects. HOW TO OBTAIN KBASE TOKEN IN FIREFOX: 1. Go to kbase.us and log in. 2. In the dashboard or narrative, press Shift+F9. Opens Storage tab of Web Developer tools. 3. In the list of cookies, click narrative.kbase.us (it may be active already). 4. Find parameter "kbase_session" (or "kbase_session_backup"). This is KBase authorization token (usually, 32 capital letters and digits). 5. Copy the token and paste into command line.
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Utility for bulk download of genomes from KBase
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