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This commit is contained in:
Eric Coissac
2025-11-16 14:56:03 +01:00
parent 35d275c104
commit 30b7175702
367 changed files with 170866 additions and 11173 deletions
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1816
jupyterhub_volumes/web/obidoc/formats/json/index.html Normal file
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jupyterhub_volumes/web/obidoc/formats/json/index.xml Normal file
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>JSON format on OBITools4 documentation</title>
<link>http://metabar:8888/obidoc/formats/json/</link>
<description>Recent content in JSON format on OBITools4 documentation</description>
<generator>Hugo</generator>
<language>en-us</language>
<atom:link href="http://metabar:8888/obidoc/formats/json/index.xml" rel="self" type="application/rss+xml" />
</channel>
</rss>

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jupyterhub_volumes/web/obidoc/formats/json/json_example.fasta Normal file
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>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct

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jupyterhub_volumes/web/obidoc/formats/json/json_example.fastq Normal file
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@AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
+
BBFFBFFHHHHHFFFFFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
@AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
+
@BBFFBFFHHHGGGFFFFFHHHJJJHHHHHHHHHJHHHHHHHHHHHHHHHHHHHHHHHHH

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jupyterhub_volumes/web/obidoc/formats/json/json_example.json Normal file
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[
{
"annotations": {
"count": 1,
"definition": "Sorex unguiculatus mitochondrial NA, complete genome.",
"family_name": "Soricidae",
"family_taxid": "9376",
"genus_name": "Sorex",
"genus_taxid": "9379",
"obicleandb_level": "family",
"obicleandb_trusted": 2.2137847111025621e-13,
"species_name": "Sorex unguiculatus",
"species_taxid": "62275",
"taxid": "62275"
},
"id": "AB061527",
"sequence": "ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct"
},
{
"annotations": {
"count": 2,
"definition": "Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.",
"family_name": "Hominidae",
"family_taxid": "9604",
"genus_name": "Homo",
"genus_taxid": "9605",
"obicleandb_level": "genus",
"obicleandb_trusted": 0,
"species_name": "Homo sapiens",
"species_taxid": "9606",
"taxid": "9606"
},
"id": "AL355887",
"sequence": "ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaacagcttaaaactcaaaggacctggcagttctttatatccct"
}
]

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jupyterhub_volumes/web/obidoc/formats/json/json_example_qual.json Normal file
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[
{
"annotations": {
"count": 1,
"definition": "Sorex unguiculatus mitochondrial NA, complete genome.",
"family_name": "Soricidae",
"family_taxid": "9376",
"genus_name": "Sorex",
"genus_taxid": "9379",
"obicleandb_level": "family",
"species_name": "Sorex unguiculatus",
"species_taxid": "62275",
"taxid": "62275"
},
"id": "AB061527",
"qualities": "BBFFBFFHHHHHFFFFFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH",
"sequence": "ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat"
},
{
"annotations": {
"count": 2,
"definition": "Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.",
"family_name": "Hominidae",
"family_taxid": "9604",
"genus_name": "Homo",
"genus_taxid": "9605",
"obicleandb_level": "genus",
"species_name": "Homo sapiens",
"species_taxid": "9606",
"taxid": "9606"
},
"id": "AL355887",
"qualities": "@BBFFBFFHHHGGGFFFFFHHHJJJHHHHHHHHHJHHHHHHHHHHHHHHHHHHHHHHHHH",
"sequence": "ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac"
}
]