Commit 6305ef3a authored by Mikael Salson's avatar Mikael Salson

format-analysis.org: Exemplify clustering

Use real example (and explain it) for clustering.
It will be tested that clones are indeed clustered.
parent 855f9c16
......@@ -105,6 +105,20 @@ and 'IMGT clonotype (AA) or (nt)' could also be used by some programs).
"5": "TRGV5*01", "5start": 0, "5end": 86,
"3": "TRGJ1*02", "3start": 89, "3end": 118
}
},
{
"id": "clone2",
"sequence": "GATACA",
"reads": [ 153, 10221 ],
"germline": "TRG",
"top": 2
},
{
"id": "clone3",
"sequence": "ATACAGA",
"reads": [ 521, 42 ],
"germline": "TRG",
"top": 3
}
]
}
......@@ -147,7 +161,7 @@ some clones, and added external data (=data=).
],
"clusters": [
[ "clone-845", "clone-821", "clone-147" ],
[ "clone2", "clone3"],
[ "clone-5", "clone-10", "clone-179" ]
],
......@@ -172,6 +186,12 @@ considered. In that case we should first consider the second point (whose =name=
is /fu1)/ and the point to be considered in second should be the first one in
the file (whose =name= is /diag/).
As exemplified in the =clusters= field, this proceeds to the clustering of
clones defined in the =.vidjil= file (here /clone2/ and /clone3/ are defined in the
vidjil file in previous section). If clones do not exist, the clusters are
just ignored. The first item of the cluster is considered as the
representative clone of the cluster.
* The different elements
** Generic information for traceability [required]
......
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