glyphs

Contains the Glyph class used to define the different type of glyphs that can be used to represent features, as well the basic plotting functions for GenomeBrowser

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Glyph

 Glyph (glyph_type:str='arrow', colors:tuple=('purple', 'orange'),
        alpha:float=0.8, show_name:bool=True, name_attr:str='gene',
        height:float=1)

A class used to define the different types of glyphs shown for different feature types.

Type Default Details
glyph_type str arrow type of the Glyph (arrow or box)
colors tuple (‘purple’, ‘orange’) can be a single color or a tuple of two colors, one for each strand
alpha float 0.8 transparency
show_name bool True
name_attr str gene default attribute to use as the name of the feature to be displayed
height float 1 height of the feature relative to other features (between 0 and 1)

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get_default_glyphs

 get_default_glyphs (arrow_colors=('purple', 'orange'),
                     box_colors=('grey',))

*Returns a dictionnary with:

  • keys: feature types (str)
  • values: a Glyph object*
default_glyphs['CDS']
Glyph object with attributes:
    glyph_type: arrow
    colors: ('purple', 'orange')
    height: 1
    alpha: 0.8
    show_name: True
    name_attr: gene

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get_patch_coordinates

 get_patch_coordinates (feature, glyphs_dict, feature_height=0.15,
                        color_attribute=None)
data_path = get_example_data_dir()
gff_path = os.path.join(data_path, "MG1655_U00096.gff3")
features=parse_gff(gff_path, 
                   feature_types=default_types, 
                   seq_id="U00096.3")[0]

features.head().apply(get_patch_coordinates, glyphs_dict=default_glyphs, axis=1)
0    (((190, 190, 190, 255, 190), (0.05, 0.2, 0.2, ...
1    (((337, 337, 2699, 2799, 2699), (0.05, 0.2, 0....
2    (((2801, 2801, 3633, 3733, 3633), (0.05, 0.2, ...
3    (((3734, 3734, 4920, 5020, 4920), (0.05, 0.2, ...
4    (((5234, 5234, 5430, 5530, 5430), (0.05, 0.2, ...
dtype: object

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html_wordwrap

 html_wordwrap (input_string:str, line_len=50, start=0)
_format_attribute("test","'UniProtKB/Swiss-Prot:P0AF03,NCBI_GP:AAC73120.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511'")
'<span style="color:DodgerBlue">test</span><span>: &#x27;UniProtKB/Swiss-Prot:P0AF03,NCBI_GP:AAC73120<br>.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511&<br>#x27;</span>'

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get_tooltip

 get_tooltip (feature, attributes, wrap=50)
features.apply(lambda row: get_tooltip(row, default_attributes),
                             axis=1)[0]
'<span style="color:FireBrick">CDS</span><br><span style="color:DodgerBlue">gene</span><span>: thrL</span><br><span style="color:DodgerBlue">locus_tag</span><span>: b0001</span><br><span style="color:DodgerBlue">product</span><span>: thr operon leader peptide</span>'
features.attributes[10]
OrderedDict([('ID', 'cds-AAC73120.1'),
             ('Parent', 'gene-b0009'),
             ('Dbxref',
              'UniProtKB/Swiss-Prot:P0AF03,NCBI_GP:AAC73120.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511'),
             ('Name', 'AAC73120.1'),
             ('gbkey', 'CDS'),
             ('gene', 'mog'),
             ('locus_tag', 'b0009'),
             ('orig_transcript_id', 'gnl|b0009|mrna.b0009'),
             ('product', 'molybdopterin adenylyltransferase'),
             ('protein_id', 'AAC73120.1'),
             ('transl_table', '11')])

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get_feature_name

 get_feature_name (row, glyphs_dict)

For each row of features DataFrame uses the Glyph object provided in the glyphs_dict to know which attribute to use as the name

features.head().apply(get_feature_name, glyphs_dict=default_glyphs, axis=1)
0    thrL
1    thrA
2    thrB
3    thrC
4    yaaX
dtype: object
#hide
gl=default_glyphs.copy()
gl["CDS"].name_attr="locus_tag"
assert features.head().apply(get_feature_name, glyphs_dict=gl, axis=1)[0]=="b0001"
assert features.loc[features.type=="repeat_region"].head().apply(get_feature_name, glyphs_dict=default_glyphs, axis=1).values[0]==''
#hide
gl["rRNA"]=Glyph(glyph_type="box", 
                        colors="red", 
                        height=0.5,
                        name_attr="locus_tag",
                        show_name=True)

print(gl["rRNA"])
features.loc[features.type=="rRNA"].head().apply(get_feature_name, glyphs_dict=gl, axis=1)
Glyph object with attributes:
    glyph_type: box
    colors: ('red',)
    height: 0.5
    alpha: 0.8
    show_name: True
    name_attr: locus_tag

235     b0201
238     b0204
239     b0205
3061    b2588
3062    b2589
dtype: object

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get_feature_patches

 get_feature_patches (features:pandas.core.frame.DataFrame, left:int,
                      right:int, glyphs_dict:dict,
                      attributes:dict=defaultdict(<function <lambda> at
                      0x7f21ecf2c430>, {'CDS': ['gene', 'locus_tag',
                      'product']}), feature_height:float=0.15,
                      label_vertical_offset:float=0.05,
                      label_justify:str='center',
                      color_attribute:str=None)
Type Default Details
features DataFrame DataFrame of the features
left int left limit
right int right limit
glyphs_dict dict a dictionary of glyphs to use for each feature type
attributes dict defaultdict(<function at 0x7f21ecf2c430>, {‘CDS’: [‘gene’, ‘locus_tag’, ‘product’]}) dictionary with feature type as keys and a list of attributes to display when hovering as values
feature_height float 0.15 fraction of the annotation track height occupied by the features
label_vertical_offset float 0.05
label_justify str center
color_attribute str None
Returns DataFrame 
patches=get_feature_patches(features,8000,12000, glyphs_dict=default_glyphs)
patches
names xs ys xbox_min color alpha pos attributes type label_y label_x
9 b0008 (8238, 8238, 9091, 9191, 9091) (0.05, 0.2, 0.2, 0.125, 0.05) 8238 purple 0.8 8714.5 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 8714.5
10 b0009 (9306, 9306, 9793, 9893, 9793) (0.05, 0.2, 0.2, 0.125, 0.05) 9306 purple 0.8 9599.5 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 9599.5
11 b0010 (10494, 10494, 10028, 9928, 10028) (0.05, 0.2, 0.2, 0.125, 0.05) 10028 orange 0.8 10211.0 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 10211.0
12 b0011 (11356, 11356, 10743, 10643, 10743) (0.05, 0.2, 0.2, 0.125, 0.05) 10743 orange 0.8 10999.5 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 10999.5
13 b0012 (10830, 10830, 11215, 11315, 11215) (0.05, 0.2, 0.2, 0.125, 0.05) 10830 purple 0.8 11072.5 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 11072.5
14 b0013 (11786, 11786, 11482, 11382, 11482) (0.05, 0.2, 0.2, 0.125, 0.05) 11482 orange 0.8 11584.0 <span style="color:FireBrick">CDS</span><br><s... CDS 0.25 11584.0