[MRG] Building databases from assembly_summary.txt #11
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Decision time! There are accessions listed in the What to do in these cases?
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is there a "quick test" target that I can run? |
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A minimal domains:
- archaea
sig_store: /group/ctbrowngrp/irber/data/wort-data/wort-genomes/sigs
db_ksizes:
- 21
db:
- refseq
bfsize:
- 1e6 |
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Starting |
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Databases calculated. They are at SBTtotal 618G GenBankRefSeqLCAtotal 2.3G GenBankRefSeq |
luizirber
changed the title
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Some comments:
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hadn't looked through this PR carefully @luizirber! The PR I put in (#15) has some bits for enabling multiple alphabets that could just be integrated here. |
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closing b/c we've completely changed up database building (for the better!) with sourmash-bio/sourmash#1885 et al. |
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Fixes #7
wort. If the signature is not available, fall back to calculate it by figuring out the download URL and streaming the data.assembly_summary.txtis downloaded for each GenBank/RefSeq domain, and used to create a catalog, a file with paths to where signatures for each accession are located.--from-file, currently using a weird syntax to extract the first signature and pass to index (and pass the others with--from-file) becauseindexrequires one signature...TODO
taxid4indexfile....sbt.zip(so I can use it with gather-to-opal)computerulecheckpointto calculate missing signatures from thesig_collectiondir?