Mercurial > repos > iuc > biobox_add_taxid
diff test-data/test-db/readme.txt @ 0:1e10251b9615 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
author | iuc |
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date | Sun, 25 Aug 2024 13:19:14 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/readme.txt Sun Aug 25 13:19:14 2024 +0000 @@ -0,0 +1,61 @@ +*.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