view x/static/js/759.9c32be0d.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

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{ ParsedLocString, parseLocString } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nexport function bufferToString(buffer: Buffer) {\n  return new TextDecoder('utf8', { fatal: true }).decode(buffer)\n}\n\nasync function parseWith(buffer: Buffer, options = {}) {\n  const csv = await import('csvtojson').then(module => module.default)\n  return csv({ noheader: true, output: 'csv', ...options }).fromString(\n    bufferToString(buffer),\n  )\n}\n\nexport interface Row {\n  id: string\n\n  extendedData?: any\n  cells: {\n    text: string\n\n    extendedData?: any\n  }[]\n}\n\nexport interface RowSet {\n  isLoaded: boolean\n  rows: Row[]\n}\n\nexport interface ParseOptions {\n  hasColumnNameLine?: boolean\n  columnNameLineNumber?: number\n  selectedAssemblyName?: string\n  isValidRefName?: (refName: string, assemblyName?: string) => boolean\n}\n\nexport interface Column {\n  name: string\n  dataType: { type: string }\n  isDerived?: boolean\n  derivationFunctionText?: string\n}\n\nfunction guessColumnType(\n  rowSet: RowSet,\n  columnNumber: number,\n  isValidRefName: (refName: string, assemblyName?: string) => boolean,\n) {\n  const text = rowSet.rows[0]!.cells[columnNumber]!.text || ''\n\n  let guessedType = 'Text'\n\n  let parsedLoc: ParsedLocString | undefined\n  try {\n    parsedLoc = parseLocString(text, isValidRefName)\n  } catch (error) {\n    //\n  }\n  if (parsedLoc?.refName && typeof parsedLoc.start === 'number') {\n    guessedType = 'LocString'\n  } else if (/^\\d+(\\.\\d+)?$/.test(text)) {\n    guessedType = 'Number'\n  }\n\n  // MAYBE TODO: iterate over the rest of the rows to confirm\n  // the type for all the rows\n\n  return guessedType\n}\n\nfunction dataToSpreadsheetSnapshot(\n  rows: string[][],\n  options: ParseOptions = {},\n) {\n  const {\n    hasColumnNameLine = false,\n    columnNameLineNumber = 1,\n    isValidRefName = () => false,\n    selectedAssemblyName,\n  } = options\n  // rows is an array of row objects and columnNames\n  // is an array of column names (in import order)\n  let maxCols = 0\n  const rowSet: RowSet = {\n    isLoaded: true,\n    rows: rows.map((row, rowNumber) => {\n      const id = rowNumber + (hasColumnNameLine ? 0 : 1)\n      if (row.length > maxCols) {\n        maxCols = row.length\n      }\n      return {\n        id: String(id),\n        cells: row.map((text, columnNumber) => {\n          return { columnNumber, text }\n        }),\n      }\n    }),\n  }\n\n  // process the column names row if present\n  const columnNames: Record<string, string> = {}\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n  if (hasColumnNameLine && columnNameLineNumber !== undefined) {\n    const [colNamesRow] = rowSet.rows.splice(columnNameLineNumber - 1, 1)\n\n    if (colNamesRow) {\n      colNamesRow.cells.forEach((cell, columnNumber) => {\n        columnNames[columnNumber] = cell.text || ''\n      })\n    }\n  }\n\n  // make our column definitions\n  const columns: Column[] = []\n  const columnDisplayOrder = []\n  for (let columnNumber = 0; columnNumber < maxCols; columnNumber += 1) {\n    columnDisplayOrder.push(columnNumber)\n    const guessedType = guessColumnType(rowSet, columnNumber, isValidRefName)\n\n    // store extendeddata for LocString column\n    if (guessedType === 'LocString') {\n      for (const row of rowSet.rows) {\n        const cell = row.cells[columnNumber]!\n        cell.extendedData = parseLocString(cell.text, isValidRefName)\n      }\n    }\n\n    columns[columnNumber] = {\n      name: columnNames[columnNumber]!,\n      dataType: {\n        type: guessedType,\n      },\n    }\n  }\n\n  return {\n    rowSet,\n    columnDisplayOrder,\n    hasColumnNames: !!hasColumnNameLine,\n    columns,\n    assemblyName: selectedAssemblyName,\n  }\n}\n\nexport async function parseCsvBuffer(buffer: Buffer, options?: ParseOptions) {\n  const rows = await parseWith(buffer)\n  return dataToSpreadsheetSnapshot(rows, options)\n}\n\nexport async function parseTsvBuffer(buffer: Buffer, options?: ParseOptions) {\n  const rows = await parseWith(buffer, { delimiter: '\\t' })\n  return dataToSpreadsheetSnapshot(rows, options)\n}\n","import { parseTsvBuffer, ParseOptions } from './ImportUtils'\nimport type { Buffer } from 'buffer'\n\nfunction parseSTARFusionBreakpointString(str: string) {\n  const fields = str.split(':')\n  const refName = fields[0]!\n  const pos = Number.parseInt(fields[1]!, 10)\n  const strand = fields[2] === '-' ? -1 : 1\n  return { refName, pos, strand }\n}\n\nconst numericColumns: Record<string, boolean> = {\n  SpanningFragCount: true,\n  FFPM: true,\n  LeftBreakEntropy: true,\n  RightBreakEntropy: true,\n  JunctionReadCount: true,\n}\n\nexport async function parseSTARFusionBuffer(\n  buffer: Buffer,\n  options: ParseOptions,\n) {\n  const data = await parseTsvBuffer(buffer, {\n    hasColumnNameLine: true,\n    columnNameLineNumber: 1,\n    selectedAssemblyName: options.selectedAssemblyName,\n    isValidRefName: () => false,\n  })\n\n  // remove the # in #FusionName\n  data.columns[0]!.name = data.columns[0]!.name.replace('#', '')\n  // set some columns to be numeric\n  data.columns.forEach(col => {\n    if (numericColumns[col.name]) {\n      col.dataType = { type: 'Number' }\n    }\n  })\n\n  // decorate each row with a feature object in its extendedData\n  data.rowSet.rows.forEach((row, rowNumber) => {\n    const featureData: Record<string, any> = {}\n    row.cells.forEach(({ text }, columnNumber) => {\n      const column = data.columns[columnNumber]!\n      if (column.name === 'LeftBreakpoint' && text) {\n        const { refName, pos, strand } = parseSTARFusionBreakpointString(text)\n        featureData.refName = refName\n        featureData.start = pos\n        featureData.end = pos\n        featureData.strand = strand\n      } else if (column.name === 'RightBreakpoint' && text) {\n        const { refName, pos, strand } = parseSTARFusionBreakpointString(text)\n        featureData.mate = {\n          refName,\n          start: pos,\n          end: pos,\n          strand,\n        }\n      } else if (text && numericColumns[column.name]) {\n        // some other column, numeric\n        featureData[column.name] = Number.parseFloat(text)\n      } else {\n        // some other column, text\n        featureData[column.name] = text\n      }\n    })\n    featureData.uniqueId = `sf-${rowNumber + 1}`\n    row.extendedData = {\n      feature: featureData,\n    }\n  })\n\n  return 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