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src/c/o/cogent-1.5.3/cogent/format/motif.py   cogent(Download)
use('Agg')  #suppress graphical rendering
 
from cogent.motif.util import MotifFormatter
from cogent.format.pdb_color import get_matching_chains,\
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
class MotifStatsBySequence(MotifFormatter):
    """Generates HTML table with Motifs organized by sequence.
 
        - Each sequence is listed as follows:
 
class MotifLocationsBySequence(MotifFormatter):
    """Generates HTML table with Motifs organized by sequence.
 
        - Each sequence is listed as follows:
 
class SequenceByMotif(MotifFormatter):
    """Generates HTML table with sequences organized by Motif.  """
 
    def __init__(self,MotifResults=None):
        """init function for MotifLocationsBySequence class"""
class HighlightMotifs(MotifFormatter):
    """Generates HTML table with sequences highlighted """
 
    def makeModuleMap(self, motif_results):
        """

src/p/y/pycogent-HEAD/cogent/format/motif.py   pycogent(Download)
use('Agg')  #suppress graphical rendering
 
from cogent.motif.util import MotifFormatter
from cogent.format.pdb_color import get_matching_chains,\
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
class MotifStatsBySequence(MotifFormatter):
    """Generates HTML table with Motifs organized by sequence.
 
        - Each sequence is listed as follows:
 
class MotifLocationsBySequence(MotifFormatter):
    """Generates HTML table with Motifs organized by sequence.
 
        - Each sequence is listed as follows:
 
class SequenceByMotif(MotifFormatter):
    """Generates HTML table with sequences organized by Motif.  """
 
    def __init__(self,MotifResults=None):
        """init function for MotifLocationsBySequence class"""
class HighlightMotifs(MotifFormatter):
    """Generates HTML table with sequences highlighted """
 
    def makeModuleMap(self, motif_results):
        """

src/c/o/cogent-1.5.3/tests/test_motif/test_util.py   cogent(Download)
#!/usr/bin/env python
#file cogent_tests/motif/test_util.py
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
    def test_getColorMapS0(self):
        """tests for getColorMapS0"""
        mf = MotifFormatter()
        module_ids = ['1','2','3','4']
        self.assertEqual(mf.getColorMapS0(module_ids),self.color_map)
 
    def test_getColorMap(self):
        """tests for getColorMap"""
        mf = MotifFormatter()
    def test_getColorMapRgb(self):
        """tests for getColorMapRgb"""
        mf = MotifFormatter()
        self.assertEqual(mf.getColorMapRgb(self.motif_results),\
            self.color_map_rgb)

src/p/y/pycogent-HEAD/tests/test_motif/test_util.py   pycogent(Download)
#!/usr/bin/env python
#file cogent_tests/motif/test_util.py
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
    def test_getColorMapS0(self):
        """tests for getColorMapS0"""
        mf = MotifFormatter()
        module_ids = ['1','2','3','4']
        self.assertEqual(mf.getColorMapS0(module_ids),self.color_map)
 
    def test_getColorMap(self):
        """tests for getColorMap"""
        mf = MotifFormatter()
    def test_getColorMapRgb(self):
        """tests for getColorMapRgb"""
        mf = MotifFormatter()
        self.assertEqual(mf.getColorMapRgb(self.motif_results),\
            self.color_map_rgb)