INNER CODE UNIT · Python

append_tbl

steineggerlab/Metabuli · util/gtdb_to_taxdump.py:214

    def append_tbl(self, table_file, join_column):
        """ appending to table """
        # creating index: name : [taxID, rank] 
        idx = {}
        self.__seen = {}
        idx['root'] = str(self.__graph_nodeIDs['root'])
        self._to_tbl_iter_idx('root', idx)
    
        # appending to file
        out_file = os.path.splitext(table_file)[0] + '_wTaxIDs.tsv'
        header = OrderedDict()
        with open(table_file) as inF, open(out_file, 'w') as outF:
            for i,line in enumerate(inF):
                line = line.rstrip().split('\t')
                if i == 0:
                    header = {x:i for i,x in enumerate(line)}
                    header['gtdb_taxid'] = len(header.keys()) + 1
                    if not join_column in header.keys():

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