Mercurial > repos > iuc > biobox_add_taxid
comparison 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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| -1:000000000000 | 0:1e10251b9615 |
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| 1 *.dmp files are bcp-like dump from GenBank taxonomy database. | |
| 2 | |
| 3 General information. | |
| 4 Field terminator is "\t|\t" | |
| 5 Row terminator is "\t|\n" | |
| 6 | |
| 7 nodes.dmp file consists of taxonomy nodes. The description for each node includes the following | |
| 8 fields: | |
| 9 tax_id -- node id in GenBank taxonomy database | |
| 10 parent tax_id -- parent node id in GenBank taxonomy database | |
| 11 rank -- rank of this node (superkingdom, kingdom, ...) | |
| 12 embl code -- locus-name prefix; not unique | |
| 13 division id -- see division.dmp file | |
| 14 inherited div flag (1 or 0) -- 1 if node inherits division from parent | |
| 15 genetic code id -- see gencode.dmp file | |
| 16 inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent | |
| 17 mitochondrial genetic code id -- see gencode.dmp file | |
| 18 inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent | |
| 19 GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage | |
| 20 hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet | |
| 21 comments -- free-text comments and citations | |
| 22 | |
| 23 Taxonomy names file (names.dmp): | |
| 24 tax_id -- the id of node associated with this name | |
| 25 name_txt -- name itself | |
| 26 unique name -- the unique variant of this name if name not unique | |
| 27 name class -- (synonym, common name, ...) | |
| 28 | |
| 29 Divisions file (division.dmp): | |
| 30 division id -- taxonomy database division id | |
| 31 division cde -- GenBank division code (three characters) | |
| 32 division name -- e.g. BCT, PLN, VRT, MAM, PRI... | |
| 33 comments | |
| 34 | |
| 35 Genetic codes file (gencode.dmp): | |
| 36 genetic code id -- GenBank genetic code id | |
| 37 abbreviation -- genetic code name abbreviation | |
| 38 name -- genetic code name | |
| 39 cde -- translation table for this genetic code | |
| 40 starts -- start codons for this genetic code | |
| 41 | |
| 42 Deleted nodes file (delnodes.dmp): | |
| 43 tax_id -- deleted node id | |
| 44 | |
| 45 Merged nodes file (merged.dmp): | |
| 46 old_tax_id -- id of nodes which has been merged | |
| 47 new_tax_id -- id of nodes which is result of merging | |
| 48 | |
| 49 Citations file (citations.dmp): | |
| 50 cit_id -- the unique id of citation | |
| 51 cit_key -- citation key | |
| 52 pubmed_id -- unique id in PubMed database (0 if not in PubMed) | |
| 53 medline_id -- unique id in MedLine database (0 if not in MedLine) | |
| 54 url -- URL associated with citation | |
| 55 text -- any text (usually article name and authors). | |
| 56 -- The following characters are escaped in this text by a backslash: | |
| 57 -- newline (appear as "\n"), | |
| 58 -- tab character ("\t"), | |
| 59 -- double quotes ('\"'), | |
| 60 -- backslash character ("\\"). | |
| 61 taxid_list -- list of node ids separated by a single space |