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Merge pull request eweitz#168 from eweitz/restore-eukaryotes-via-eutils
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Fully restore support for eukaryotes
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@eweitz
eweitz authored Aug 30, 2019
2 parents ebad875 + a2e197f commit 147a812
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10 changes: 5 additions & 5 deletions examples/vanilla/eukaryotes.html
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Expand Up @@ -49,7 +49,7 @@ <h1>Eukaryotes | Ideogram</h1>
<li><label for="rattus-norvegicus"><input type="radio" name="org" value="rattus-norvegicus" id="rattus-norvegicus">Rat (Rattus norvegicus)</label></li>
<li><label for="drosophila-melanogaster"><input type="radio" name="org" value="drosophila-melanogaster" id="drosophila-melanogaster">Fly (Drosophila melanogaster)</label>
<li><label for="caenorhabditis-elegans"><input type="radio" name="org" value="caenorhabditis-elegans" id="caenorhabditis-elegans">Worm (Caenorhabditis elegans)</label></li>
<!-- <li><label for="danio-rerio"><input type="radio" name="org" value="danio-rerio" id="danio-rerio">Zebrafish (Danio rerio)</label></li> -->
<li><label for="danio-rerio"><input type="radio" name="org" value="danio-rerio" id="danio-rerio">Zebrafish (Danio rerio)</label></li>
<li><label for="arabidopsis-thaliana"><input type="radio" name="org" value="arabidopsis-thaliana" id="arabidopsis-thaliana">Thale cress (Arabidopsis thaliana)</label></li>
<li><label for="saccharomyces-cerevisiae"><input type="radio" name="org" value="saccharomyces-cerevisiae" id="saccharomyces-cerevisiae">Yeast (Saccharomyces cerevisiae)</label></li>
</ul>
Expand All @@ -63,18 +63,18 @@ <h1>Eukaryotes | Ideogram</h1>
<!-- <li><label for="canis-lupus-familiaris"><input type="radio" name="org" value="canis-lupus-familiaris" id="canis-lupus-familiaris">Dog (Canis lupus familiaris)</label></li> -->
<!-- <li><label for="gallus-gallus"><input type="radio" name="org" value="gallus-gallus" id="gallus-gallus">Chicken (Gallus gallus)</label></li> -->
<!-- <li><label for="bos-taurus"><input type="radio" name="org" value="bos-taurus" id="bos-taurus">Cow (Bos taurus)</label></li> -->
<!-- <li><label for="sus-scrofa"><input type="radio" name="org" value="sus-scrofa" id="sus-scrofa">Pig (Sus scrofa)</label></li> -->
<li><label for="sus-scrofa"><input type="radio" name="org" value="sus-scrofa" id="sus-scrofa">Pig (Sus scrofa)</label></li>
</ul>
</li>
<li>
Plants
<ul>
<li><label for="zea-mays"><input type="radio" name="org" value="zea-mays" id="zea-mays">Maize (Zea mays)</label></li>
<li><label for="oryza-sativa"><input type="radio" name="org" value="oryza-sativa" id="oryza-sativa">Rice (Oryza sativa)</label>
<!-- <li><label for="solanum-lycopersicum"><input type="radio" name="org" value="solanum-lycopersicum" id="solanum-lycopersicum">Tomato (Solanum lycopersicum)</label></li> -->
<li><label for="solanum-lycopersicum"><input type="radio" name="org" value="solanum-lycopersicum" id="solanum-lycopersicum">Tomato (Solanum lycopersicum)</label></li>
<li><label for="musa-acuminata"><input type="radio" name="org" value="musa-acuminata" id="musa-acuminata">Banana (Musa acuminata)</label></li>
<!-- <li><label for="vitis-vinifera"><input type="radio" name="org" value="vitis-vinifera" id="vitis-vinifera">Grape (Vitis vinifera)</label></li> -->
<li><label for="micromonas-commoda"><input type="radio" name="org" value="micromonas-commoda" id="micromonas-commoda">Green algae</label></li>
<li><label for="vitis-vinifera"><input type="radio" name="org" value="vitis-vinifera" id="vitis-vinifera">Grape (Vitis vinifera)</label></li>
<li><label for="micromonas-commoda"><input type="radio" name="org" value="micromonas-commoda" id="micromonas-commoda">Green algae (Micromonas commoda)</label></li>
</ul>
</li>
<li>
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177 changes: 89 additions & 88 deletions src/js/services/services.js
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Original file line number Diff line number Diff line change
@@ -1,83 +1,54 @@
import {d3, hasGenBankAssembly} from '../lib';
import {d3} from '../lib';
import {
esearch, esummary, elink, getAssemblySearchUrl
} from './eutils-config.js';
import {
getTaxids, getOrganismFromEutils
} from './organisms.js';

function getNuccoreQueryString(gbUid, asmUid, recovering, ideo) {
/**
* Get a URL to ESearch the NCBI Nucleotide DB for an Assembly UID
*/
function getESearchUrlForChromosomes(asmUid, ideo) {
var qs;

// Get a list of IDs for the chromosomes in this genome.
//
// If this is our first pass, or if assembly is GenBank-only, or if
// a GenBank assembly was explicitly requested (GCA_), then query RefSeq
// sequences in Nucleotide DB. Otherwise, query the lesser-known
// GenColl (Genomic Collections) DB.
if (hasGenBankAssembly(ideo) || typeof recovering !== 'undefined') {
// TODO: account for GenBank-only
qs = '&db=nuccore&linkname=assembly_nuccore_insdc&from_uid=' + asmUid;
} else {
qs = '&db=nuccore&linkname=assembly_nuccore_refseq&from_uid=' + asmUid;
}

return qs;
}
// Query chromosomes sequences in Nucleotide DB (nuccore) via
// Assembly DB E-Utils link.
qs = ('&db=nuccore&dbfrom=assembly&linkname=assembly_nuccore&' +
'cmd=neighbor_history&from_uid=' + asmUid);

function getAssemblyAndNuccoreLink(data, asmAndChrArray, recovering, ideo) {
var assembly, qs, gbUid, nuccoreLink, asmUid;

asmUid = data.result.uids[0];
assembly = data.result[asmUid];
// rsUid = assembly.rsuid; // RefSeq UID for this assembly
gbUid = assembly.gbuid; // GenBank UID

asmAndChrArray.push(assembly.assemblyaccession);

qs = getNuccoreQueryString(gbUid, asmUid, recovering, ideo);
nuccoreLink = ideo.elink + qs;

return [asmAndChrArray, nuccoreLink];
return d3.json(ideo.elink + qs)
.then(function(data) {
var webenv = data.linksets[0].webenv;
qs =
'&db=nuccore' +
'&term=%231+AND+%28' +
'sequence_from_chromosome[Properties]+OR+' +
'sequence_from_plastid[Properties]+OR+' +
'sequence_from_mitochondrion[Properties]%29' +
'&WebEnv=' + webenv + '&usehistory=y&retmax=1000';
return ideo.esearch + qs;
});
}

/**
* If the list of presumed chromosomes is longer than 100 elements, then
* we've likely fetched scaffolds instead of chromosomes. This
* happens with e.g. Sus scrofa (pig). Try recovering once via a
* different query, and throw an error upon any subsequent failure.
* Request basic data on a list of chromosome IDs from ESearch
*/
function handleScaffoldData(data, asmAndChrArray, context) {
var assemblyAccession = asmAndChrArray[0],
linksets = data.linksets[0],
ideo = context.ideo;
if ('linksetdbs' in linksets && linksets.linksetdbs[0].links.length > 100) {
if (typeof context.recovering === 'undefined') {
ideo.getAssemblyAndChromosomesFromEutils(context.callback, true);
return Promise.reject(
'Unexpectedly found genomic scaffolds instead of chromosomes ' +
'while querying RefSeq. Recovering.'
);
} else {
// Avoid flooding NCBI with EUtils requests.
throw Error(
'Failed to find chromosomes for genome ' + assemblyAccession
);
}
}
}

function fetchNucleotideSummary(data, assemblyAccession, context) {
var links, ntSummary;

handleScaffoldData(data, assemblyAccession, context);

links = data.linksets[0].linksetdbs[0].links.join(',');
ntSummary = context.ideo.esummary + '&db=nucleotide&id=' + links;

function fetchNucleotideSummary(data, ideo) {
var ids, ntSummary;
ids = data.esearchresult.idlist.join(',');
ntSummary = ideo.esummary + '&db=nucleotide&id=' + ids;
return d3.json(ntSummary);
}

/**
* Get name and type for mitochondrial chromosome
*
* See example of "MT" in yeast:
* https://eweitz.github.io/ideogram/eukaryotes?org=saccharomyces-cerevisiae
*/
function parseMitochondrion(result, ideo) {
var type, cnIndex, chrName;

Expand All @@ -101,6 +72,12 @@ function parseMitochondrion(result, ideo) {
return [chrName, type];
}

/**
* Get name and type for chloroplastic chromosome.
*
* Plants have chloroplasts. See e.g. green algae:
* https://eweitz.github.io/ideogram/eukaryotes?org=micromonas-commoda
*/
function parseChloroplastOrPlastid(ideo) {
// Plastid encountered with rice genome IRGSP-1.0 (GCF_001433935.1)
if (ideo.config.showNonNuclearChromosomes) {
Expand All @@ -109,13 +86,24 @@ function parseChloroplastOrPlastid(ideo) {
return [null, null];
}

/**
* Get name and type for apicoplast chromosome
*
* Plasmodium falciparum (malaria parasite) has such a chromosome, see e.g.:
* https://eweitz.github.io/ideogram/eukaryotes?org=plasmodium-falciparum
*/
function parseApicoplast(ideo) {
if (ideo.config.showNonNuclearChromosomes) {
return ['AP', 'apicoplast'];
}
return [null, null];
}

/**
* Get name and type for nuclear chromosome
*
* These are typical chromosomes, like chromosome 1.
*/
function parseNuclear(result) {
var type, cnIndex, chrName;

Expand All @@ -131,6 +119,9 @@ function parseNuclear(result) {
return [chrName, type];
}

/**
* Get name and type of any chromosome object from NCBI Nucleotide ESummary
*/
function getChrNameAndType(result, ideo) {
var genome = result.genome;
if (genome === 'mitochondrion') {
Expand Down Expand Up @@ -158,27 +149,36 @@ function parseChromosome(result, ideo) {
return chromosome;
}

function parseChromosomes(results, asmAndChrArray, ideo) {
var x, chromosome,
function parseChromosomes(results, ideo) {
var x, chromosome, seenChrId,
seenChrs = {},
chromosomes = [];

for (x in results) {
// omit list of result uids
if (x === 'uids') continue;

chromosome = parseChromosome(results[x], ideo);
chromosomes.push(chromosome);
seenChrId = chromosome.name + '_' + chromosome.length;
if (chromosome.type !== null && seenChrId in seenChrs === false) {
// seenChrs accounts for duplicate chromosomes seen with
// pig (Sus scrofa), likely GenBank and RefSeq copies.
chromosomes.push(chromosome);
}

seenChrs[seenChrId] = 1;
}

chromosomes = chromosomes.sort(Ideogram.sortChromosomes);

ideo.coordinateSystem = 'bp';

asmAndChrArray.push(chromosomes);

return asmAndChrArray;
return chromosomes;
}

/**
* Request ESummary data from an ESearch on a genome assembly
*/
function fetchAssemblySummary(data, ideo) {
var asmUid, asmSummaryUrl;

Expand All @@ -190,34 +190,35 @@ function fetchAssemblySummary(data, ideo) {
}

/**
* Returns names and lengths of chromosomes for an organism's best-known
* genome assembly, or for a specified assembly. Gets data from NCBI
* EUtils web API.
* Returns assembly accession, as well as names and lengths of chromosomes for
* an organism's best-known genome assembly, or for a specified assembly.
*
* Gets data from NCBI EUtils web API.
*
* @param callback Function to call upon completion of this async method
* @param recovering Boolean indicating attempt at failure recovery
*/
function getAssemblyAndChromosomesFromEutils(callback, recovering) {
var asmSearchUrl, nuccoreLink,
asmAndChrArray = [],
ideo = this,
context = {callback: callback, recovering: recovering, ideo: ideo};

asmSearchUrl = getAssemblySearchUrl(ideo);

function getAssemblyAndChromosomesFromEutils(callback) {
var assemblyAccession,
ideo = this;

// Search for assembly, then
// get summary of that assembly, then
// get search URL for chromosomes in that assembly, then
// get search results containing chromosome IDs, then
// get summaries of each of those chromosome IDs, then
// format the chromosome summaries and pass them into callback function.
var asmSearchUrl = getAssemblySearchUrl(ideo);
d3.json(asmSearchUrl)
.then(function(data) { return fetchAssemblySummary(data, ideo); })
.then(function(data) {
[asmAndChrArray, nuccoreLink] =
getAssemblyAndNuccoreLink(data, asmAndChrArray, recovering, ideo);
return d3.json(nuccoreLink);
})
.then(function(data) {
return fetchNucleotideSummary(data, asmAndChrArray, context);
})
var asmUid = data.result.uids[0];
assemblyAccession = data.result[asmUid];
return getESearchUrlForChromosomes(asmUid, ideo);
}).then(function(esearchUrl) { return d3.json(esearchUrl); })
.then(function(data) { return fetchNucleotideSummary(data, ideo); })
.then(function(data) {
asmAndChrArray = parseChromosomes(data.result, asmAndChrArray, ideo);
return callback(asmAndChrArray);
var chromosomes = parseChromosomes(data.result, ideo);
return callback([assemblyAccession, chromosomes]);
}, function(rejectedReason) {
console.warn(rejectedReason);
});
Expand Down
1 change: 0 additions & 1 deletion src/js/views/chromosome-labels.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ import {d3} from '../lib';

function getChrSetLabelLines(d, i, ideo) {
var lines;

if (d.name.indexOf(' ') === -1) {
lines = [d.name];
} else {
Expand Down
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