# from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
# from obitools3.dms.dms import OBIDMS       # TODO cimport doesn't work
# from obitools3.utils cimport bytes2str
# 
# import time
# import re


def run(config):
    pass

# __title__="Export a NUC_SEQS view to a fasta or fastq file"
# 
# 
# default_config = {   'inputview'    : None,
#                  }
# 
# def addOptions(parser):
# 
#     # TODO put this common group somewhere else but I don't know where
#     group=parser.add_argument_group('DMS and view options')
# 
#     group.add_argument('--default-dms','-d', 
#                        action="store", dest="obi:defaultdms",
#                        metavar='<DMS NAME>',
#                        default=None,
#                        type=str,
#                        help="Name of the default DMS for reading and writing data.")
# 
#     group.add_argument('--input-view','-i',
#                        action="store", dest="obi:inputview",
#                        metavar='<INPUT VIEW NAME>',
#                        default=None,
#                        type=str,
#                        help="Name of the input view, either raw if the view is in the default DMS,"
#                             " or in the form 'dms:view' if it is in another DMS.")
# 
#     group=parser.add_argument_group('obi export specific options')
# 
#     group.add_argument('--format','-f',
#                        action="store", dest="export:format",
#                        metavar='<FORMAT>',
#                        default="fasta",
#                        type=str,
#                        help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.")         # TODO export in csv
# 
# def run(config):
#     
#     # TODO import doesn't work
#     NUC_SEQUENCE_COLUMN = "NUC_SEQ"
#     ID_COLUMN = "ID"
#     DEFINITION_COLUMN = "DEFINITION"
#     QUALITY_COLUMN = "QUALITY"    
#     
#     special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
#     
#     # Open DMS
#     d = OBIDMS(config['obi']['defaultdms'])
#     
#     # Open input view
#     iview = d.open_view(config['obi']['inputview'])
#     
#     print(iview.type)
#     
#     # TODO check that the view has the type NUC_SEQS
#     if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") :   # TODO find a way to import those macros
#         raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
#     
#     # Initialize the progress bar
#     pb = ProgressBar(len(iview), config, seconde=5)
#     
#     i=0
#     for seq in iview :
#         pb(i)
#         
#         toprint = ">"+seq.id+" "
#         
#         for col_name in seq :
#             if col_name not in special_columns :
#                 toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
#         
#         if DEFINITION_COLUMN in seq :
#             toprint = toprint + seq.definition
#         
#         nucseq = bytes2str(seq.nuc_seq)
#         
#         if config['export']['format'] == "fasta" :
#             nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
#         
#         toprint = toprint + "\n" + nucseq
#         
#         if config['export']['format'] == "fastq" :
#             toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
#             
#         print(toprint)
#         i+=1
#         
#     iview.close()
#     d.close()
#     
#     print("Done.")
#     
#     
# 
#     
#     
#     
#     
#