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Commit 6ff6546e authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-format.md: document seg.junction.unproductive

closes #4674
parent b224db00
Pipeline #211686 passed with stages
in 41 minutes and 41 seconds
......@@ -388,17 +388,20 @@ In the `.analysis` file, this section is intended to describe some specific clon
// - "seq" : a sequence
// - "val" : a numerical value
// - "info" : a textual vlaue
//
// JUNCTION//CDR3 should be stored that way (in fields called "junction" of "cdr3"),
// its productivity must be stored in a boolean field called "productive".
// "seq" field should not be filled for cdr3 or junction (it is extracted from the sequence itself).
// However a "aa" field may be used to give the amino-acid translation of the cdr3 or junction.
"somefeature": { "start": 56, "stop": 61, "seq": "ACTGTA", "val": 145.7, "info": "analyzed with xyz" },
// Numerical or textual features concerning all the sequence or its analysis (such as 'evalue')
// can be provided by omitting "start" and "stop" elements.
"someotherfeature": {"val": 0.004521},
"anotherfeature": {"info": "VH CDR3 stereotypy"},
// JUNCTION//CDR3 should be stored that way (in fields called "junction" or "cdr3"),
// Its productivity must be stored in a boolean field called "productive".
// When the sequence is not productive, the "unproductive" field may contain the reason (mainly "stop-codon" or "out-of-frame")
// "seq" field should not be filled for cdr3 or junction (it is extracted from the sequence itself).
// However a "aa" field may be used to give the amino-acid translation of the cdr3 or junction.
"junction": { "start": 41, "stop": 82, "aa": "CATWDRKNYYKKLF", "productive": false, "unproductive": "stop-codon" },
}
......
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