Commit 7ca256b9 authored by Jan Keller's avatar Jan Keller
Browse files

Documentation for GI retriever gi.py

parent 93fb5165
.. highlight:: yaml
Gene Identifier
====
Retrieve GI xml documents for dbxrefs and convert them into json.
Options
-------
* ``--basics`` - Include basic informations such as dbxref/accession-nr., locus, source organism and definition.
* ``--dbsource`` - Include source database information.
* ``--references`` - Include reference information.
Input
-----
example: ``GI:P0ABT0``
Output
------
output scheme::
[
{
"dbxref": "GI:P0ABT0",
"definition": "RecName: Full=DNA polymerase III subunit theta",
"locus": "HOLE_ECO57",
"molecular_info": null,
"organism": {
"name": "Escherichia coli",
"taxonomy": null
},
"references": [
{
"authors": [
"Perna, N.T.",
"Plunkett, G.",
"Burland, V.",
"Mau, B.",
"Glasner, J.D.",
"Rose, D.J.",
"Mayhew, G.F.",
"Evans, P.S.",
"Gregor, J.",
"Kirkpatrick, H.A.",
"Posfai, G.",
"Hackett, J.",
"Klink, S.",
"Boutin, A.",
"Shao, Y.",
"Miller, L.",
"Grotbeck, E.J.",
"Davis, N.W.",
"Lim, A.",
"Dimalanta, E.T.",
"Potamousis, K.D.",
"Apodaca, J.",
"Anantharaman, T.S.",
"Lin, J.",
"Yen, G.",
"Schwartz, D.C.",
"Welch, R.A.",
"Blattner, F.R."
],
"doi": "10.1038/35054089",
"journal": {
"date": "25.1.2001",
"name": "Nature"
},
"title": "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7."
},
{
"authors": [
"Hayashi, T.",
"Makino, K.",
"Ohnishi, M.",
"Kurokawa, K.",
"Ishii, K.",
"Yokoyama, K.",
"Han, C.G.",
"Ohtsubo, E.",
"Nakayama, K.",
"Murata, T.",
"Tanaka, M.",
"Tobe, T.",
"Iida, T.",
"Takami, H.",
"Honda, T.",
"Sasakawa, C.",
"Ogasawara, N.",
"Yasunaga, T.",
"Kuhara, S.",
"Shiba, T.",
"Hattori, M.",
"Shinagawa, H."
],
"doi": "10.1093/dnares/8.1.11",
"journal": {
"date": "28.2.2001",
"name": "DNA Res."
},
"title": "Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12."
}
],
"source databases": [
"SMR:P0ABT0",
"STRING:155864.EDL933_2815",
"EnsemblBacteria:AAG56832",
"EnsemblBacteria:AAG56832",
"EnsemblBacteria:Z2891",
"EnsemblBacteria:BAB35975",
"EnsemblBacteria:BAB35975",
"EnsemblBacteria:BAB35975",
"GeneID:913059",
"KEGG:ece:Z2891",
"KEGG:ecs:ECs2552",
"PATRIC:fig|386585.9.peg.2675",
"eggNOG:ENOG4105MPK",
"eggNOG:ENOG4111UZC",
"HOGENOM:HOG000219272",
"KO:K02345",
"BioCyc:ECOO157:HOLE-MONOMER",
"Proteomes:UP000000558",
"Proteomes:UP000002519",
"GO:GO:0003677",
"GO:GO:0003887",
"GO:GO:0006260",
"Gene3D:1.20.58.250",
"InterPro:IPR009052",
"InterPro:IPR036745",
"Pfam:PF06440"
],
"structure": null
}
]
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment