Fast taxtable #87
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Fast taxtable #87
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commit a051e0e Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 23 13:55:14 2016 -0700 added some function comments commit 2b38851 Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 23 12:55:25 2016 -0700 created species_is_classified function commit 5f03f38 Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 23 12:54:56 2016 -0700 making this less loud commit badac7a Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 21 16:29:02 2016 -0700 Removed --append-lineage. Rest of script is MUCH faster using Pandas. commit b2b9338 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 21 16:27:31 2016 -0700 ranks indexed from lowest to highest in database table for sorting later commit 7fdc05d Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 21 16:26:22 2016 -0700 --from-taxid and --from-taxtable are now --from-id and --from-table commit 7ba03ec Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 16 16:24:46 2016 -0700 moved to subcommand taxtable commit 8be153d Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 16 16:07:13 2016 -0700 refreshing unittests, data was stale and incomplete commit abdc319 Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 16 14:44:52 2016 -0700 taxid not valid as of 2014 http://www.ncbi.nlm.nih.gov/taxonomy/?term=477972 commit 7ee2f4d Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 14 14:55:48 2016 -0700 moving a couple log messages commit d9819d2 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 14 14:42:36 2016 -0700 without pruning commit 0834539 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 14 14:41:08 2016 -0700 faster way to build ncbi taxonomy. Includes initial taxonomic pruning. commit 7d84d67 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Sep 14 14:40:08 2016 -0700 adding database schema back and removing building of full taxtable commit 19d4c91 Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 2 17:19:28 2016 -0700 building full taxtable with Pandas and inserting into database commit 0cb37bd Author: Chris Rosenthal <crosenth@uw.edu> Date: Fri Sep 2 17:19:05 2016 -0700 clobber ncbi database as well if --clobber
…er with lowest rank having the sql index of 0
… the case in ncbi releases in the fungal kingdom
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Need to generate a report of all the intermediate ranks above species (below_ ranks) to decide if we should just drop them entirely and reset the effected nodes' parent_ids. |
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Generate some taxtables between this and master and do some md5sums to make sure the output is exactly the same. |
… nodes that depend on other new nodes
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About a month's worth of work for two goals, speed up
taxit taxtableand additional functionality fortaxit add_nodes. One update is the ncbi_taxonomy.db is a required positional argument rather than an optional argument for many for subcommandas new_database, update_taxids and add_nodes. There is also a new RANKS table in the ncbi_taxonomy.db which holds a hierarchy of taxonomic ranks.