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src/c/o/cogent-1.5.3/cogent/app/dotur.py   cogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.format.table import phylipMatrix
from cogent.parse.dotur import OtuListParser
 
 
    #Get phylip formatted string.
    phylip_matrix_string = phylipMatrix(rows=d_matrix_list,names=order)
 
    working_dir = get_tmp_filename(suffix='')

src/p/y/pycogent-HEAD/cogent/app/dotur.py   pycogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.format.table import phylipMatrix
from cogent.parse.dotur import OtuListParser
 
 
    #Get phylip formatted string.
    phylip_matrix_string = phylipMatrix(rows=d_matrix_list,names=order)
 
    working_dir = get_tmp_filename(suffix='')

src/c/o/cogent-1.5.3/cogent/util/table.py   cogent(Download)
            formatted_table = [row[self._row_ids:] for row in formatted_table]
            header = header[self._row_ids:]
            return table_format.phylipMatrix(formatted_table, header)
        elif format == 'bedgraph':
            assert self.Shape[1] == 4, 'bedgraph format is for 4 column tables'

src/p/y/pycogent-HEAD/cogent/util/table.py   pycogent(Download)
            formatted_table = [row[self._row_ids:] for row in formatted_table]
            header = header[self._row_ids:]
            return table_format.phylipMatrix(formatted_table, header)
        elif format == 'bedgraph':
            assert self.Shape[1] == 4, 'bedgraph format is for 4 column tables'

src/c/o/cogent-1.5.3/cogent/app/clearcut.py   cogent(Download)
from cogent.core.tree import PhyloNode
from cogent.util.dict2d import Dict2D
from cogent.format.table import phylipMatrix
 
__author__ = "Jeremy Widmann"
            row.append(str(int_map_dists[key1][key2]))
        rows.append(row)
    input_matrix = phylipMatrix(rows, names)
    #input needs a trailing whitespace or it will fail!
    input_matrix += '\n'

src/p/y/pycogent-HEAD/cogent/app/clearcut.py   pycogent(Download)
from cogent.core.tree import PhyloNode
from cogent.util.dict2d import Dict2D
from cogent.format.table import phylipMatrix
 
__author__ = "Jeremy Widmann"
            row.append(str(int_map_dists[key1][key2]))
        rows.append(row)
    input_matrix = phylipMatrix(rows, names)
    #input needs a trailing whitespace or it will fail!
    input_matrix += '\n'