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Initial work of ESM transformation

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be5invis 2022-07-16 19:26:49 -07:00
parent 2472c9cff2
commit b8205a63aa
303 changed files with 1959 additions and 2450 deletions
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238
utility/export-data/ligation-data.mjs Normal file
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import fs from "fs";
import path from "path";
import * as toml from "@iarna/toml";
const ligationSamples = [
[
"-<<",
"-<",
"-<-",
"<--",
"<---",
"<<-",
"<-",
"->",
"->>",
"-->",
"--->",
"->-",
">-",
">>-",
"<->",
"<-->",
"<--->",
"<---->",
"<!--"
],
[
"=<<",
"=<",
"=<=",
"<==",
"<===",
"<<=",
"<=",
"=>",
"=>>",
"==>",
"===>",
"=>=",
">=",
">>=",
"<=>",
"<==>",
"<===>",
"<====>",
"<!---"
],
[
"[|",
"|]",
"{|",
"|}",
"<=<",
">=>",
"<~~",
"<~",
"~>",
"~~>",
"::",
":::",
"\\/",
"/\\",
"==",
"!=",
"/=",
`~=`,
`<>`,
"===",
"!==",
"=/=",
"=!=",
":>"
],
[
":=",
":-",
":+",
"<*",
"<*>",
"*>",
"<|",
"<|>",
"|>",
"<.",
"<.>",
".>",
"+:",
"-:",
"=:",
"<***>",
"__",
"(* comm *)",
"++",
"+++",
"|-",
"-|"
]
];
const ligationSamplesNarrow = [
[
"-<<",
"-<",
"-<-",
"<--",
"<---",
"<<-",
"<-",
"->",
"->>",
"-->",
"--->",
"->-",
">-",
">>-"
],
[
"=<<",
"=<",
"=<=",
"<==",
"<===",
"<<=",
"<=",
"=>",
"=>>",
"==>",
"===>",
"=>=",
">=",
">>="
],
["<->", "<-->", "<--->", "<---->", "<=>", "<==>", "<===>", "<====>", "-------->"],
[
"<~~",
"<~",
"~>",
"~~>",
"::",
":::",
"==",
"!=",
"/=",
`~=`,
`<>`,
"===",
"!==",
"=/=",
"=!="
],
[
":=",
":-",
":+",
"<*",
"<*>",
"*>",
"<|",
"<|>",
"|>",
"<.",
"<.>",
".>",
"+:",
"-:",
"=:",
":>",
"__"
],
[
"(*",
"*)",
"[|",
"|]",
"{|",
"|}",
"++",
"+++",
"\\/",
"/\\",
"|-",
"-|",
"<!--",
"<!---",
"<***>"
]
];
function buildLigationSet(ligData, getKey) {
const ligationSets = new Map([
["*off", { tag: "calt", rank: 0, desc: "Ligation Off", brief: "Off", ligSets: [] }]
]);
for (const sel in ligData.composite) {
const comp = ligData.composite[sel];
if (!comp.tag) continue;
const key = getKey(comp);
let item = ligationSets.get(key);
if (!item) {
let ligSets = new Set();
for (const s of comp.buildup) {
ligSets.add(ligData.simple[s].ligGroup);
}
item = {
selector: sel,
tag: comp.tag,
rank: 1,
ligSets: [...ligSets],
tagName: [comp.tag],
desc: comp.desc,
brief: comp.brief || comp.desc
};
ligationSets.set(key, item);
} else {
item.tagName = [...item.tagName, comp.tag];
item.desc += ", " + comp.desc;
item.brief += ", " + comp.brief;
}
}
return ligationSets;
}
export const parseLigationData = async function () {
const ligToml = await fs.promises.readFile(
path.join(__dirname, "../../params/ligation-set.toml"),
"utf8"
);
const ligData = toml.parse(ligToml);
const ligationSets = buildLigationSet(ligData, comp => comp.buildup.join(","));
const nonMergeLigationSets = buildLigationSet(
ligData,
comp => comp.tag + comp.buildup.join(",")
);
return {
samples: ligationSamples,
samplesNarrow: ligationSamplesNarrow,
cherry: ligData.simple,
rawSets: ligData.composite,
sets: [...ligationSets.values()],
nonMergeSets: [...nonMergeLigationSets.values()]
};
};