# Path: checkm/common.py
# def checkFileExists(inputFile):
#     """Check if file exists."""
#     if not os.path.exists(inputFile):
#         logger = logging.getLogger('timestamp')
#         logger.error('Input file does not exists: ' + inputFile + '\n')
#         sys.exit(1)
# 
# def reassignStdOut(outFile):
#     """Redirect standard out to a file."""
#     oldStdOut = sys.stdout
#     if(outFile != ''):
#         try:
#             # redirect stdout to a file
#             sys.stdout = open(outFile, 'w')
#         except:
#             logger = logging.getLogger('timestamp')
#             logger.error("Error diverting stdout to file: " + outFile)
#             sys.exit(1)
# 
#     return oldStdOut
# 
# def restoreStdOut(outFile, oldStdOut):
#     """Redirect standard out back to system standard out."""
#     if(outFile != ''):
#         try:
#             # redirect stdout to a file
#             sys.stdout.close()
#             sys.stdout = oldStdOut
#         except:
#             logger = logging.getLogger('timestamp')
#             logger.error("Error restoring stdout ", outFile)
#             sys.exit(1)


import logging
import checkm.prettytable
from checkm.defaultValues import DefaultValues
from checkm.common import checkFileExists, reassignStdOut, restoreStdOut

            pTable.vrules = prettytable.NONE

        for binId in sortedBinIds:
            row = [binId]
            row += [float(binSize[binId]) / 1e6]

            for bamId in sortedBamIds:
                row += [readsMappedToBin[binId][bamId]]
                row += [perMappedReads[binId][bamId] * 100.0]

                if DefaultValues.UNBINNED in perMappedReads:
                    unbinnedPercentage = perMappedReads[DefaultValues.UNBINNED][bamId]
                else:
                    unbinnedPercentage = 0

                if binId == DefaultValues.UNBINNED:
                    row += ['NA']
                    row += [unbinnedPercentage * 100.0]
                else:
                    row += [normBinCoverage[binId][bamId] * 100.0]
                    row += [normBinCoverage[binId][bamId] * 100.0 * (1.0 - unbinnedPercentage)]

            if bTabTable:
                print('\t'.join(list(map(str, row))))
            else:
                pTable.add_row(row)

        if not bTabTable:
            print(pTable.get_string())


# Path: checkm/common.py
# def checkFileExists(inputFile):
#     """Check if file exists."""
#     if not os.path.exists(inputFile):
#         logger = logging.getLogger('timestamp')
#         logger.error('Input file does not exists: ' + inputFile + '\n')
#         sys.exit(1)
# 
# def reassignStdOut(outFile):
#     """Redirect standard out to a file."""
#     oldStdOut = sys.stdout
#     if(outFile != ''):
#         try:
#             # redirect stdout to a file
#             sys.stdout = open(outFile, 'w')
#         except:
#             logger = logging.getLogger('timestamp')
#             logger.error("Error diverting stdout to file: " + outFile)
#             sys.exit(1)
# 
#     return oldStdOut
# 
# def restoreStdOut(outFile, oldStdOut):
#     """Redirect standard out back to system standard out."""
#     if(outFile != ''):
#         try:
#             # redirect stdout to a file
#             sys.stdout.close()
#             sys.stdout = oldStdOut
#         except:
#             logger = logging.getLogger('timestamp')
#             logger.error("Error restoring stdout ", outFile)
#             sys.exit(1)


# Path: checkm/profile.py
import logging
import checkm.prettytable
from checkm.defaultValues import DefaultValues
from checkm.common import checkFileExists, reassignStdOut, restoreStdOut

            pTable.vrules = prettytable.NONE

        for binId in sortedBinIds:
            row = [binId]
            row += [float(binSize[binId]) / 1e6]

            for bamId in sortedBamIds:
                row += [readsMappedToBin[binId][bamId]]
                row += [perMappedReads[binId][bamId] * 100.0]

                if DefaultValues.UNBINNED in perMappedReads:
                    unbinnedPercentage = perMappedReads[DefaultValues.UNBINNED][bamId]
                else:
                    unbinnedPercentage = 0

                if binId == DefaultValues.UNBINNED:
                    row += ['NA']
                    row += [unbinnedPercentage * 100.0]
                else:
                    row += [normBinCoverage[binId][bamId] * 100.0]
                    row += [normBinCoverage[binId][bamId] * 100.0 * (1.0 - unbinnedPercentage)]

            if bTabTable:
                print('\t'.join(list(map(str, row))))
            else:
                pTable.add_row(row)

        if not bTabTable:
            print(pTable.get_string())


        restoreStdOut(outFile, oldStdOut)
