Commit eb717275 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/format-analysis.org: 'info' textual fields in 'seg' features

Some external tools would like to provide sequence features with textual information.
Discussion with @flothoni and @duez.
parent b117328f
......@@ -304,21 +304,24 @@ In the =.analysis= file, this section is intended to describe some specific clon
// Positions on the sequence start at 1.
{
"5": {"name": "IGHV5*01", "start": 1, "stop": 120}, // V (or 5') segment
"4": {"name": "IGHD1*01", "start": 124, "stop": 135}, // D (or middle) segment
"4": {"name": "IGHD1*01", "start": 124, "stop": 135, "info": "unsure designation"}, // D (or middle) segment
// Recombination with several D may use "4a", "4b"...
"3": {"name": "IGHJ3*02", "start": 136, "stop": 171}, // J (or 3') segment
// any feature to be highlighted in the sequence
// the optional "seq" element gives a sequence that corresponds to this feature,
// and the optional "val" element gives a numerical value.
// any feature to be highlighted in the sequence, with optional fields related to this feature:
// - "start"/"stop" : positions on the clone sequence (starting at 1)
// - "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".
// Positions also start at 1.
"somefeature": { "start": 56, "stop": 61, "seq": "ACTGTA", "val": 145.7 },
"somefeature": { "start": 56, "stop": 61, "seq": "ACTGTA", "val": 145.7, "info": "analyzed with xyz" },
// Numerical features concerning all the sequence or its analysis (such as 'evalue')
// 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"},
}
......
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