@datagrok/sequence-translator 1.0.17 → 1.1.4

package/src/hardcode-to-be-eliminated/ICDs.ts

@@ -1,3 +0,0 @@
-export const ICDS = `DISPLAY
-NO DATA
-`;

package/src/hardcode-to-be-eliminated/IDPs.ts

@@ -1,3 +0,0 @@
-export const IDPS = `DISPLAY
-NO DATA
-`;

package/src/hardcode-to-be-eliminated/const.ts

@@ -1,5 +0,0 @@
-import * as map from './map';
-
-export const MODIFICATIONS = map.MODIFICATIONS;
-
-export const standardPhosphateLinkSmiles = 'OP(=O)(O)O';

package/src/hardcode-to-be-eliminated/constants.ts

@@ -1,101 +0,0 @@
-const RNA_COLOR = 'rgb(255,230,153)';
-const INVABASIC_COLOR = 'rgb(203,119,211)';
-export const AXOLABS_MAP:
-  {[index: string]: {fullName: string, symbols: [string, string, string, string], color: string}} =
-{
-  'RNA': {
-    fullName: 'RNA nucleotides',
-    symbols: ['A', 'C', 'G', 'U'],
-    color: RNA_COLOR,
-  },
-  'DNA': {
-    fullName: 'DNA nucleotides',
-    symbols: ['dA', 'dC', 'dG', 'dT'],
-    color: 'rgb(197,224,180)',
-  },
-  "2\"-Fluoro": {
-    fullName: '2\'-Fluoro nucleotides',
-    symbols: ['Af', 'Cf', 'Gf', 'Uf'],
-    color: 'rgb(68,114,196)',
-  },
-  "2\"-O-Methyl": {
-    fullName: '2\'-O-Methyl nucleotides',
-    symbols: ['a', 'c', 'g', 'u'],
-    color: 'rgb(166,166,166)',
-  },
-  "2\"-O-MOE": {
-    fullName: '2\'-O-MOE nucleotides (including 5-Methyl C)',
-    symbols: ['Am', 'Cm', 'Gm', 'Tm'],
-    color: 'rgb(112,48,160)',
-  },
-  'GNA': {
-    fullName: 'Glycol nucleic acid',
-    symbols: ['(GNA-A)', '(GNA-C)', '(GNA-G)', '(GNA-T)'],
-    color: 'rgb(255,192,0)',
-  },
-  'LNA': {
-    fullName: 'Locked nucleic acid (including 5-Methyl C)',
-    symbols: ['Ab', 'Cb', 'Gb', 'Tb'],
-    color: 'rgb(54,229,238)',
-  },
-  'UNA': {
-    fullName: 'Unlocked nucleotides',
-    symbols: ['Ao', 'Co', 'Go', 'Uo'],
-    color: 'rgb(255,192,0)',
-  },
-  'A': {
-    fullName: 'Adenosine',
-    symbols: ['a', 'a', 'a', 'a'],
-    color: RNA_COLOR,
-  },
-  'C': {
-    fullName: 'Cytidine',
-    symbols: ['c', 'c', 'c', 'c'],
-    color: RNA_COLOR,
-  },
-  'G': {
-    fullName: 'Guanosine',
-    symbols: ['g', 'g', 'g', 'g'],
-    color: RNA_COLOR,
-  },
-  'U': {
-    fullName: 'Uridine',
-    symbols: ['u', 'u', 'u', 'u'],
-    color: RNA_COLOR,
-  },
-  'X-New': {
-    fullName: '',
-    symbols: ['X', 'X', 'X', 'X'],
-    color: 'rgb(108,0,0)',
-  },
-  'Y-New': {
-    fullName: '',
-    symbols: ['Y', 'Y', 'Y', 'Y'],
-    color: 'rgb(210,146,146)',
-  },
-  'Z-New': {
-    fullName: '',
-    symbols: ['Z', 'Z', 'Z', 'Z'],
-    color: 'rgb(155,108,132)',
-  },
-  'InvAbasic': {
-    fullName: 'Inverted abasic capped',
-    symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
-    color: INVABASIC_COLOR,
-  },
-  "5\"-vinylps": {
-    fullName: '5\'-vinylphosphonate-2\'-OMe-uridine',
-    symbols: ['(vinu)', '(vinu)', '(vinu)', '(vinu)'],
-    color: 'rgb(0,0,139)',
-  },
-  'InvAbasic(o)': {
-    fullName: 'Inverted abasic capped (overhang)',
-    symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
-    color: INVABASIC_COLOR,
-  },
-  "2\"-OMe-U(o)": {
-    fullName: 'Nucleotide Uridine with 2\'O-Methyl protection (overhang)',
-    symbols: ['mU', 'mU', 'mU', 'mU'],
-    color: 'rgb(65,233,80)',
-  },
-};

package/src/hardcode-to-be-eliminated/converters.ts

@@ -1,323 +0,0 @@
-import {lcmsToGcrs, MODIFICATIONS} from './map';
-import * as DG from 'datagrok-api/dg';
-import {DELIMITER} from './map';
-import {sortByStringLengthInDescendingOrder} from '../utils/helpers';
-//name: gcrsToLcms
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: LCMS}
-export function gcrsToLcms(sequence: string): string {
-  try {
-    const df = DG.DataFrame.fromCsv(lcmsToGcrs);
-    const arr1: string[] = df.getCol('GCRS').toList();
-    const arr2: string[] = df.getCol('LCMS').toList();
-    const obj: { [i: string]: string } = {};
-    arr1.forEach((element, index) => obj[element] = arr2[index]);
-    obj[DELIMITER] = DELIMITER;
-    const codes = arr1
-      .concat(DELIMITER)
-      .concat(Object.keys(MODIFICATIONS));
-    const sortedCodes = sortByStringLengthInDescendingOrder(codes);
-    let i = 0;
-    let r1 = '';
-    while (i < sequence.length) {
-      const matchedCode = sortedCodes.find((c) => c == sequence.slice(i, i + c.length))!;
-      r1 += obj[sequence.slice(i, i + matchedCode.length)];
-      i += matchedCode.length;
-    }
-    while (r1.indexOf('//') != -1)
-      r1 = r1.replace('//', '/');
-    return r1;
-  } catch {
-    return '<error>';
-  }
-}
-
-//name: asoGapmersNucleotidesToBioSpring
-//input: string nucleotides {semType: DNA nucleotides}
-//output: string result {semType: BioSpring / Gapmers}
-export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
-  let count: number = -1;
-  const objForEdges: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': '5*', 'A': '6*', 'C': '7*', 'G': '8*'};
-  const objForCenter: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'T*', 'A': 'A*', 'C': '9*', 'G': 'G*'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|C|G)/g, function(x: string) {
-    count++;
-    return (count > 4 && count < 15) ? objForCenter[x] : objForEdges[x];
-  }).slice(0, (nucleotides.endsWith('(invabasic)') || nucleotides.endsWith('(GalNAc-2-JNJ)')) ?
-    nucleotides.length : 2 * count + 1);
-}
-
-//name: asoGapmersNucleotidesToGcrs
-//input: string nucleotides {semType: DNA nucleotides}
-//output: string result {semType: GCRS / Gapmers}
-export function asoGapmersNucleotidesToGcrs(nucleotides: string): string {
-  let count: number = -1;
-  const objForEdges: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'moeUnps',
-    'A': 'moeAnps', 'C': 'moe5mCnps', 'G': 'moeGnps'};
-  const objForCenter: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'C': '5mCps', 'A': 'Aps', 'T': 'Tps', 'G': 'Gps'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|C|G)/g, function(x: string) {
-    count++;
-    if (count < 5) return (count == 4) ? objForEdges[x].slice(0, -3) + 'ps' : objForEdges[x];
-    if (count < 15) return (count == 14) ? objForCenter[x].slice(0, -2) + 'nps' : objForCenter[x];
-    return objForEdges[x];
-  }).slice(0, (nucleotides.endsWith('(invabasic)') || nucleotides.endsWith('(GalNAc-2-JNJ)')) ?
-    nucleotides.length : -3);
-}
-
-//name: asoGapmersBioSpringToNucleotides
-//input: string nucleotides {semType: BioSpring / Gapmers}
-//output: string result {semType: DNA nucleotides}
-export function asoGapmersBioSpringToNucleotides(nucleotides: string): string {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '*': '', '5': 'T', '6': 'A', '7': 'C', '8': 'G', '9': 'C'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|5|6|7|8|9)/g, function(x: string) {return obj[x];});
-}
-
-//name: asoGapmersBioSpringToGcrs
-//input: string nucleotides {semType: BioSpring / Gapmers}
-//output: string result {semType: GCRS / Gapmers}
-export function asoGapmersBioSpringToGcrs(nucleotides: string): string {
-  let count: number = -1;
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '5*': 'moeUnps', '6*': 'moeAnps', '7*': 'moe5mCnps', '8*': 'moeGnps', '9*': '5mCps', 'A*': 'Aps', 'T*': 'Tps',
-    'G*': 'Gps', 'C*': 'Cps', '5': 'moeU', '6': 'moeA', '7': 'moe5mC', '8': 'moeG',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|5\*|6\*|7\*|8\*|9\*|A\*|T\*|G\*|C\*|5|6|7|8)/g,
-    function(x: string) {
-      count++;
-      return (count == 4) ? obj[x].slice(0, -3) + 'ps' : (count == 14) ? obj[x].slice(0, -2) + 'nps' : obj[x];
-    });
-}
-
-
-//name: asoGapmersGcrsToBioSpring
-//input: string nucleotides {semType: GCRS / Gapmers}
-//output: string result {semType: BioSpring / Gapmers}
-export function asoGapmersGcrsToBioSpring(nucleotides: string): string {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': '1', 'fA': '2', 'fC': '3', 'fG': '4', 'mU': '5', 'mA': '6', 'mC': '7', 'mG': '8',
-    'moeT': '5', 'moeA': '6', 'moe5mC': '7', 'moeG': '8', 'moeU': '5', '5mC': '9', 'nps': '*', 'ps': '*', 'U': 'T',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|moeT|moeA|moe5mC|moeG|moeU|5mC|nps|ps|U)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: asoGapmersGcrsToNucleotides
-//input: string nucleotides {semType: GCRS / Gapmers}
-//output: string result {semType: DNA nucleotides}
-export function asoGapmersGcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'moe': '', '5m': '', 'n': '', 'ps': '', 'U': 'T'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|moe|5m|n|ps|U)/g, function(x: string) {return obj[x];});
-}
-
-//name: siRnaBioSpringToNucleotides
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: RNA nucleotides}
-export function siRnaBioSpringToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'U', '2': 'A', '3': 'C', '4': 'G', '5': 'U', '6': 'A', '7': 'C', '8': 'G', '*': ''};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaBioSpringToAxolabs
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: Axolabs / siRNA}
-export function siRnaBioSpringToAxolabs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'Uf', '2': 'Af', '3': 'Cf', '4': 'Gf', '5': 'u', '6': 'a', '7': 'c', '8': 'g', '*': 's'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-
-//name: siRnaBioSpringToGcrs
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: GCRS}
-export function siRnaBioSpringToGcrs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'fU', '2': 'fA', '3': 'fC', '4': 'fG', '5': 'mU', '6': 'mA', '7': 'mC', '8': 'mG', '*': 'ps'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToGcrs
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: GCRS}
-export function siRnaAxolabsToGcrs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': 'fU', 'Af': 'fA', 'Cf': 'fC', 'Gf': 'fG', 'u': 'mU', 'a': 'mA', 'c': 'mC', 'g': 'mG', 's': 'ps',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToBioSpring
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaAxolabsToBioSpring(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': '1', 'Af': '2', 'Cf': '3', 'Gf': '4', 'u': '5', 'a': '6', 'c': '7', 'g': '8', 's': '*',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToNucleotides
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: RNA nucleotides}
-export function siRnaAxolabsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': 'U', 'Af': 'A', 'Cf': 'C', 'Gf': 'G', 'u': 'U', 'a': 'A', 'c': 'C', 'g': 'G', 's': '',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-
-//name: siRnaGcrsToNucleotides
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: RNA nucleotides}
-export function siRnaGcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': 'U', 'fA': 'A', 'fC': 'C', 'fG': 'G', 'mU': 'U', 'mA': 'A', 'mC': 'C', 'mG': 'G', 'ps': '',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaGcrsToBioSpring
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaGcrsToBioSpring(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': '1', 'fA': '2', 'fC': '3', 'fG': '4', 'mU': '5', 'mA': '6', 'mC': '7', 'mG': '8', 'ps': '*',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaGcrsToAxolabs
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: Axolabs / siRNA}
-export function siRnaGcrsToAxolabs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': 'Uf', 'fA': 'Af', 'fC': 'Cf', 'fG': 'Gf', 'mU': 'u', 'mA': 'a', 'mC': 'c', 'mG': 'g', 'ps': 's',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaNucleotideToBioSpringSenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaNucleotideToBioSpringSenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '6*', 'U': '5*', 'G': '8*', 'C': '7*'};
-  const objForRightEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '*6', 'U': '*5', 'G': '*8', 'C': '*7'};
-  const objForOddIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '6', 'U': '5', 'G': '8', 'C': '7'};
-  const objForEvenIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': '2', 'U': '1', 'G': '4', 'C': '3'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count > nucleotides.length - 3) return objForRightEdge[x];
-    return (count % 2 == 0) ? objForEvenIndices[x] : objForOddIndices[x];
-  });
-}
-
-//name: siRnaNucleotidesToGcrs
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: GCRS}
-export function siRnaNucleotidesToGcrs(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'mAps', 'U': 'mUps', 'G': 'mGps', 'C': 'mCps'};
-  const objForRightEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'psmA', 'U': 'psmU', 'G': 'psmG', 'C': 'psmC'};
-  const objForEvenIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'fA', 'U': 'fU', 'G': 'fG', 'C': 'fC'};
-  const objForOddIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'mA', 'U': 'mU', 'G': 'mG', 'C': 'mC'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count > nucleotides.length - 3) return objForRightEdge[x];
-    return (count % 2 == 0) ? objForEvenIndices[x] : objForOddIndices[x];
-  });
-}
-
-//name: siRnaNucleotideToAxolabsSenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: Axolabs}
-export function siRnaNucleotideToAxolabsSenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'as', 'U': 'us', 'G': 'gs', 'C': 'cs'};
-  const objForSomeIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Af', 'U': 'Uf', 'G': 'Gf', 'C': 'Cf'};
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'a', 'U': 'u', 'G': 'g', 'C': 'c'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count == 6 || (count > 7 && count < 11)) return objForSomeIndices[x];
-    if (count == nucleotides.length - 1) return 'a';
-    return obj[x];
-  });
-}
-
-//name: siRnaNucleotideToAxolabsAntisenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: Axolabs}
-export function siRnaNucleotideToAxolabsAntisenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForSmallLinkages: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'as', 'U': 'us', 'G': 'gs', 'C': 'cs'};
-  const objForBigLinkages: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Afs', 'U': 'Ufs', 'G': 'Gfs', 'C': 'Cfs'};
-  const objForSomeIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Af', 'U': 'Uf', 'G': 'Gf', 'C': 'Cf'};
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'a', 'U': 'u', 'G': 'g', 'C': 'c'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count > 19 && count < 22) return objForSmallLinkages[x];
-    if (count == 0) return 'us';
-    if (count == 1) return objForBigLinkages[x];
-    return (count == 5 || count == 7 || count == 8 || count == 13 || count == 15) ? objForSomeIndices[x] : obj[x];
-  });
-}
-
-//name: gcrsToNucleotides
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: RNA nucleotides}
-export function gcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'mAps': 'A', 'mUps': 'U', 'mGps': 'G', 'mCps': 'C', 'fAps': 'A', 'fUps': 'U', 'fGps': 'G', 'fCps': 'C',
-    'fU': 'U', 'fA': 'A', 'fC': 'C', 'fG': 'G', 'mU': 'U', 'mA': 'A', 'mC': 'C', 'mG': 'G',
-  };
-  return nucleotides.replace(
-    /(\(invabasic\)|\(GalNAc-2-JNJ\)|mAps|mUps|mGps|mCps|fAps|fUps|fGps|fCps|fU|fA|fC|fG|mU|mA|mC|mG)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: gcrsToMermade12
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: Mermade 12 / siRNA}
-export function gcrsToMermade12(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'mAps': 'e', 'mUps': 'h', 'mGps': 'g', 'mCps': 'f', 'fAps': 'i', 'fUps': 'l', 'fGps': 'k', 'fCps': 'j', 'fU': 'L',
-    'fA': 'I', 'fC': 'J', 'fG': 'K', 'mU': 'H', 'mA': 'E', 'mC': 'F', 'mG': 'G',
-  };
-  return nucleotides.replace(
-    /(\(invabasic\)|\(GalNAc-2-JNJ\)|mAps|mUps|mGps|mCps|fAps|fUps|fGps|fCps|fU|fA|fC|fG|mU|mA|mC|mG)/g,
-    function(x: string) {return obj[x];});
-}