Mercurial > repos > iuc > biobox_add_taxid
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
author | iuc |
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date | Sun, 08 Sep 2024 14:37:41 +0000 |
parents | 1e10251b9615 |
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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