ideogram/src/js/bands/parse.js

Chromosome visualization for the web

function getDelimiterTsvLinesAndInit(source, content) {
  var delimiter, tsvLines, init;

  if (typeof chrBands === 'undefined' && source !== 'native') {
    delimiter = /\t/;
    tsvLines = content.split(/\r\n|\n/);
    init = 1;
  } else {
    delimiter = / /;
    tsvLines = content;
    init = 0;
  }

  return [delimiter, tsvLines, init];
}

function updateChromosomes(chromosomes) {
  var tmp, i;

  if (chromosomes instanceof Array && typeof chromosomes[0] === 'object') {
    tmp = [];
    for (i = 0; i < chromosomes.length; i++) {
      tmp.push(chromosomes[i].name);
    }
    chromosomes = tmp;
  }
  return chromosomes;
}

function getLineObject(chr, columns, stain, taxid) {
  return {
    chr: chr,
    bp: {
      start: parseInt(columns[5], 10),
      stop: parseInt(columns[6], 10)
    },
    iscn: {
      start: parseInt(columns[3], 10),
      stop: parseInt(columns[4], 10)
    },
    px: {
      start: -1,
      stop: -1,
      width: -1
    },
    name: columns[1] + columns[2],
    stain: stain,
    taxid: taxid
  };
}

function getStain(columns) {
  var stain = columns[7];
  // For e.g. acen and gvar, columns[8] (density) is undefined
  if (columns[8]) stain += columns[8];
  return stain;
}

function updateLines(lines, columns, taxid) {
  var chr, stain, line;

  chr = columns[0];
  if (chr in lines === false) lines[chr] = [];

  stain = getStain(columns);

  line = getLineObject(chr, columns, stain, taxid);
  lines[chr].push(line);

  return lines;
}

/**
 * Reports if a cytogenetic band should be included in parse results
 *
 * TODO:
 * Normalize ideogram.chromosomes upstream.
 *
 * This function is complex because ideogram.chromosomes is (likely
 * unnecessarily) complex.  The "ideogram.chromosomes" object can
 * take many forms depending on the use case, and this results in
 * hard-to-reason-about functions like this.
 *
 * Normalizing ideogram.chromosomes to a common format somewhere upstream
 * would likely make this specific function and Ideogram in general much
 * more maintainable.
 */
function shouldSkipBand(chrs, chr, taxid, ideo) {

  var hasChrs, chrsAreList, chrNotInList, chrsAreObject,
    innerChrsAreStrings, matchingChrObjs, chrNotInObject,
    multiorganism = ideo.config.multiorganism;

  hasChrs = typeof chrs !== 'undefined' && chrs !== null;
  if (!hasChrs) return false;

  chrsAreList = Array.isArray(chrs);
  chrNotInList = chrsAreList && chrs.indexOf(chr) === -1;
  chrsAreObject = typeof chrs === 'object';

  if (chrsAreList && !chrsAreObject && chrNotInList) return true;

  if (taxid in chrs === false && multiorganism) return false;

  if (!multiorganism) {
    // Encountered in single organism when showing subset of all chromosomes,
    // e.g. only human X and Y as in https://eweitz.github.io/ideogram/homology-basic
    matchingChrObjs = chrs.filter(thisChr => thisChr === chr);
    chrNotInObject = matchingChrObjs.length === 0;
  } else {
    innerChrsAreStrings = typeof chrs[taxid][0] === 'string';
    if (innerChrsAreStrings) {
      chrNotInObject = chrs[taxid].includes(chr) === false;
    } else {
      matchingChrObjs = chrs[taxid].filter(thisChr => thisChr.name === chr);
      chrNotInObject = matchingChrObjs.length === 0;
    }
  }
  return chrNotInObject;

}

/**
 * Parses cytogenetic band data from a TSV file, or, if band data is
 * prefetched, from an array
 *
 * NCBI:
 * #chromosome arm band iscn_start iscn_stop bp_start bp_stop stain density
 * ftp://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_9606_GCF_000001305.14_550_V1
 */
function parseBands(taxid, chromosomes, ideo) {
  var delimiter, tsvLines, columns, chr, i, init, source, content,
    lines = {};

  content = ideo.bandData[taxid];

  if (Array.isArray(content)) source = 'native';

  chromosomes = updateChromosomes(chromosomes);

  // Destructure assignment fails oddly when transpiled.  2019-05-23
  var result = getDelimiterTsvLinesAndInit(source, content);
  delimiter = result[0];
  tsvLines = result[1];
  init = result[2];

  for (i = init; i < tsvLines.length; i++) {
    columns = tsvLines[i].split(delimiter);

    chr = columns[0];
    if (shouldSkipBand(chromosomes, chr, taxid, ideo)) {
      // If specific chromosomes are configured, then skip processing all
      // other fetched chromosomes.
      continue;
    }

    lines = updateLines(lines, columns, taxid);
  }

  return lines;
}

export {parseBands};