diff test-data/test-db/readme.txt @ 0:0fd79958fac6 draft

planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82

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+*.dmp files are bcp-like dump from GenBank taxonomy database.
+
+General information.
+Field terminator is "\t|\t"
+Row terminator is "\t|\n"
+
+nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
+fields:
+	tax_id					-- node id in GenBank taxonomy database
+ 	parent tax_id				-- parent node id in GenBank taxonomy database
+ 	rank					-- rank of this node (superkingdom, kingdom, ...) 
+ 	embl code				-- locus-name prefix; not unique
+ 	division id				-- see division.dmp file
+ 	inherited div flag  (1 or 0)		-- 1 if node inherits division from parent
+ 	genetic code id				-- see gencode.dmp file
+ 	inherited GC  flag  (1 or 0)		-- 1 if node inherits genetic code from parent
+ 	mitochondrial genetic code id		-- see gencode.dmp file
+ 	inherited MGC flag  (1 or 0)		-- 1 if node inherits mitochondrial gencode from parent
+ 	GenBank hidden flag (1 or 0)            -- 1 if name is suppressed in GenBank entry lineage
+ 	hidden subtree root flag (1 or 0)       -- 1 if this subtree has no sequence data yet
+ 	comments				-- free-text comments and citations
+
+Taxonomy names file (names.dmp):
+	tax_id					-- the id of node associated with this name
+	name_txt				-- name itself
+	unique name				-- the unique variant of this name if name not unique
+	name class				-- (synonym, common name, ...)
+
+Divisions file (division.dmp):
+	division id				-- taxonomy database division id
+	division cde				-- GenBank division code (three characters)
+	division name				-- e.g. BCT, PLN, VRT, MAM, PRI...
+	comments
+
+Genetic codes file (gencode.dmp):
+	genetic code id				-- GenBank genetic code id
+	abbreviation				-- genetic code name abbreviation
+	name					-- genetic code name
+	cde					-- translation table for this genetic code
+	starts					-- start codons for this genetic code
+
+Deleted nodes file (delnodes.dmp):
+	tax_id					-- deleted node id
+
+Merged nodes file (merged.dmp):
+	old_tax_id                              -- id of nodes which has been merged
+	new_tax_id                              -- id of nodes which is result of merging
+
+Citations file (citations.dmp):
+	cit_id					-- the unique id of citation
+	cit_key					-- citation key
+	pubmed_id				-- unique id in PubMed database (0 if not in PubMed)
+	medline_id				-- unique id in MedLine database (0 if not in MedLine)
+	url					-- URL associated with citation
+	text					-- any text (usually article name and authors).
+						-- The following characters are escaped in this text by a backslash:
+						-- newline (appear as "\n"),
+						-- tab character ("\t"),
+						-- double quotes ('\"'),
+						-- backslash character ("\\").
+	taxid_list				-- list of node ids separated by a single space