Example of how to convert biom format data to a tsv file

convert_biom_to_tsv.py

# requires the package 'json-stream'
import json_stream
import os
import shutil

scratchDir = "scratch"

def get_biom_row_count(biomFileName):
  biomFile = open(biomFileName)
  biomData = json_stream.load(biomFile)

  shape = biomData["shape"]
  rowCount = shape[0]
  columnCount = shape[1]

  biomFile.close()

  return rowCount, columnCount

def build_tsv_file(biomFileName, tsvFileName):
  rowCount, columnCount = get_biom_row_count(biomFileName)
  tsvFile = open(f"{scratchDir}/{tsvFileName}", "w")

  for rowIdx in range(rowCount):
    rowFile = open(f"{scratchDir}/{rowIdx}")
    columns = []

    for _ in range(columnCount + 1):
      columns.append("0.0")

    for columnDataStr in rowFile.readlines():
      columnData = columnDataStr.split(",")
      columnIdx = int(columnData[0])
      columnValue = columnData[1].replace("\n", "")

      if columnIdx != 0:
        columnValue = f"{float(columnValue)}"

      columns[columnIdx] = columnValue

    rowFile.close()

    tsvFile.write("\t".join(columns))
    tsvFile.write("\n")

  tsvFile.close()

def dump_biom_rows(biomFileName):
  biomFile = open(biomFileName)
  biomData = json_stream.load(biomFile)

  manualRowIdx = 0

  for row in biomData["rows"]:
    rowId = row["id"]

    rowHandle = open(f"{scratchDir}/{manualRowIdx}", "w")
    rowHandle.write(f"0,{rowId}\n")
    rowHandle.close()

    manualRowIdx = manualRowIdx + 1

  for dataRow in biomData["data"]:
    rowIdx = dataRow[0]

    rowHandle = open(f"{scratchDir}/{rowIdx}", "a")
    rowHandle.write(f"{dataRow[1] + 1},{dataRow[2]}\n")
    rowHandle.close()

  biomFile.close()

def init_scratch_dir():
  if os.path.isdir(scratchDir):
    shutil.rmtree(scratchDir)

  os.makedirs(scratchDir)

init_scratch_dir()
dump_biom_rows("min_sparse_otu_table.biom")
build_tsv_file("min_sparse_otu_table.biom", "min_sparse_otu_table.tsv")