MSAViewer¶

class visualife.widget.MSAViewer(element_id, msa_header='', msa=None, **kwargs)¶

Bases: object

Displays a Multiple Sequence Alignment (MSA)

A basic example of the widget is given below:

It has been created by the following code:

from visualife.widget import MSAViewer

msa = [ {"description" : "Crambin", "sequence": "TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN"},
{"description" : "Thionin", "sequence": "-SCCPTTAARNTYNVCRLPGTPRPVCASLSGCIIISGTRCPPNYPR"},
{"description" : "Viscotoxin", "sequence": "-SCCPNTTGRNIYNTCRFGGGSREVCASLSGCKIISASTCP-SYPD"}]

msa = MSAViewer("show_msa","crambin homologs", msa=msa)
msa.add_to_region("sel1", 1, first_pos=4, last_pos=8)
msa.region_tooltip("sel1","first region")

Parameters:

element_id – id of div element where you want to display your MSA
msa_header – header text will be display on top of MSA
msa – list of dictionaries; each dictionary is another sequence; eg. {“description”:”2gb1”,”sequence”:”AGTPTACAGA”}

Keyword Arguments:

if_bars (bool) – if True bars will appeare under every part of MSA
bars_function (string) – name of a function that bars shows
n_columns_of_ten (int) – when the widget displays sequence, it puts a space after every 10 residues; by default there are 50 residues in every line, divided in five 10-residues blocks; say n_columns_of_ten=4 to display only 40 residues per line or to n_columns_of_ten=8 if you like to have 80 residues per line
show_blockwise (bool) – if True, a sequence will be displayed in blocks of 10 residues, separated by a space (True by default); otherwise, each row of this widget will be a contiguous line of amino acid or nucleotide symbols

Attributes Summary

`msa_header`	Header line for this MSA
`secondary_structure`	Protein / nucleotide secondary structure - for coloring purposes only

Methods Summary

`aa_composition`(i_column)	Returns amino acid composition of a given column of this alignment.
`add_to_region`(region_name, which_sequence[, …])	Add a block of amino acids/nucleotides to a sequence region
`async_viewer`(res)
`change_bars`(what)
`color_background`(color_scheme, **kwargs)	Color letter background of this MSA
`color_sequences`(color_scheme, **kwargs)	Color letters of this MSA
`colors_by_scheme`(color_scheme[, which_sequence])	Returns a vector of colors to color this MSA.
`hydrophobicity`(i_column)	Computes average hydrophobicity at a given position for the most probable residue
`identity_fraction`(i_column)	Computes sequence identity fraction at a given position for the most probable residue :param i_column: index of an alignment column (from 0) :return: a two-tuple of the most probable residue code and the fraction of sequences it has been observed in that column
`load_msa`(msa_as_json[, msa_header, …])	Loads MSA data into this widget.
`region_tooltip`(region_name, tooltip)	Sets a text that will show up in a tooltip
`shannon_entropy`(i_column)	Computes Shannon entropy for a given column of this alignment.

Attributes Documentation

msa_header¶

Header line for this MSA

Getter:	returns the header line displayed by the widget
Setter:	sets the new header line string
Type:	string

secondary_structure¶

Protein / nucleotide secondary structure - for coloring purposes only

Getter:	returns the secondary structure
Setter:	sets secondary structure string for this sequence
Type:	string

Methods Documentation

aa_composition(i_column)¶

Returns amino acid composition of a given column of this alignment.

Parameters:	i_column – index of an alignment column (from 0)
Returns:	a dictionary with single-letter characters as keys and integer counts as avalues

add_to_region(region_name, which_sequence, if_show_region=True, **kwargs)¶

Add a block of amino acids/nucleotides to a sequence region

This method calls SequenceViewer.add_to_region() method of an appropriate SequenceViewer panel of this widget. :param region_name: name of this sequence region :param which_sequence: (integer) index of a sequence to mark a region; use 0 (the default)

to mark a region on all sequences shown by this widget

Parameters:	if_show_region – if True, the sequence region will be made visible after this change kwargs – see `SequenceViewer.add_to_region()` documentation

async_viewer(res)¶

change_bars(what)¶

color_background(color_scheme, **kwargs)¶

Color letter background of this MSA

Parameters:

color_scheme –
either a color scheme name or a list of colors separately for each sequence: - (string) – a color scheme name the available color schemes are listed in colors_by_scheme()

method documentation
- (list[float]) – list of values to be converted to colors with a given palette; the same color will be used for a given column
- (list[list[float]]) – list of values to be converted to colors with a given palette
- (list[list[string]]) – list of colors to be used directly to color this MSA
kwargs – see below

Keyword Arguments:

palette_name (string) – name of a color palette used to convert values into colors
neutral_color (string) – a color to be used when no color can be assigned; white is used by default

color_sequences(color_scheme, **kwargs)¶

Color letters of this MSA

Parameters:

color_scheme –
either a color scheme name or a list of colors separately for each sequence: - (string) – a color scheme name the available color schemes are listed in colors_by_scheme()

method documentation
- (list[list[float]]) – list of values to be converted to colors with a given palette
- (list[list[string]]) – list of colors to be used directly to color this MSA
kwargs – see below

Keyword Arguments:

palette_name (string) – name of a color palette used to convert values into colors
neutral_color (string) – a color to be used when no color can be assigned; black is used by default

colors_by_scheme(color_scheme, which_sequence=0, **kwargs)¶

Returns a vector of colors to color this MSA.

This method calculates color schemes based on MSA composition rather than on a single amino acid type. To color residues by chemical type, use method from SequenceViewer class

Known color schemes:
Parameters:	color_scheme – a color scheme name; known schemes are listed below which_sequence – a sequence to be used as a reference; kwargs – see below
	secondary – color by secondary structure which must be provided by a `secondary_structure()` setter identity – color scale based on the sequence identity (conservation) of a given MSA column entropy – color scale based on the Shanon entropy of a given MSA column hydrophobicity – color scale based on the average hydrophobicity of a given MSA column mutations – color amino acids that are very unlikely in a given MSA column
Keyword Arguments:
	palette_name (`string`) – name of a color palette used to convert values into colors neutral_color (`string`) – a color to be used when no color can be assigned; a typical choice is `"black"` to color letters and `"white"` for background
Returns:	`list[str]` list of `n_res` colors, where `n_res` is the length of the selected sequence if a given `color_scheme` is incorrect, an emtpy list is returned

hydrophobicity(i_column)¶

Computes average hydrophobicity at a given position for the most probable residue

Parameters:	i_column – index of an alignment column (from 0)
Returns:	average hydrophobicity according to Kyte & Doolittle scale

identity_fraction(i_column)¶: Computes sequence identity fraction at a given position for the most probable residue :param i_column: index of an alignment column (from 0) :return: a two-tuple of the most probable residue code and the fraction of sequences it has been observed

in that column

load_msa(msa_as_json, msa_header='', fix_terminal_gaps=True, **kwargs)¶

Loads MSA data into this widget.

Input sequences should be provided in JSON data structure, see read_fasta() method for details :param msa_as_json: input sequences :param msa_header: a string displayed at the top of the MSA widget to describe it

region_tooltip(region_name, tooltip)¶

Sets a text that will show up in a tooltip

The given text will be displayed in a tooltip box when a user hoovers the given sequence region with a mouse pointer. Use empty string to clear a tooltip

Parameters:	region_name – name of a sequence region that needs a tooltip tooltip – tooltip text

shannon_entropy(i_column)¶

Computes Shannon entropy for a given column of this alignment.

Parameters:	i_column – index of an alignment column (from 0)
Returns:	information entropy value in the range of [0,1]