jdna.viewer¶

Classes to view sequences.

The viewer can display sequences and annotations, as in the following:

> "Unnamed" (550bp)


                                                            ----------------GFP----------------
                                                            |<START
                                                            ----      -----------RFP-----------
0         CCCAGGACTAGCGACTTTCCGTAACGCGACCTAACACCGGCCGTTCCTTCGAGCCAGGCAAATGTTACGTCACTTCCTTAGATTT
          GGGTCCTGATCGCTGAAAGGCATTGCGCTGGATTGTGGCCGGCAAGGAAGCTCGGTCCGTTTACAATGCAGTGAAGGAATCTAAA

          ------GFP------
          -----------------------------------------RFP-----------------------------------------
85        TGAACAGCGCCGTACCCCGATATGATATTTAGATATATAGCAGTTACACTTGGGGTTGCTATGGACTTAGATCTGCTGTATGTTT
          ACTTGTCGCGGCATGGGGCTATACTATAAATCTATATATCGTCAATGTGAACCCCAACGATACCTGAATCTAGACGACATACAAA

          -----------------------------------------RFP-----------------------------------------
170       TCTTACCTTCCGCATCAGGGGACAATTCGCCAGTAGAATTCAGTTTGTGCGTGAGAACATAAGATTGAATCCCACGCAGGCACAA
          AGAATGGAAGGCGTAGTCCCCTGTTAAGCGGTCATCTTAAGTCAAACACGCACTCTTGTATTCTAACTTAGGGTGCGTCCGTGTT

          ---------------------RFP----------------------
255       GCAGGGCGGGCAGACTCTATAGGTCCTAAGACCCTGAGACTGCGTCCTCAAGATACAGGTTAACAATCCCCGTATGGAGCCGTTC
          CGTCCCGCCCGTCTGAGATATCCAGGATTCTGGGACTCTGACGCAGGAGTTCTATGTCCAATTGTTAGGGGCATACCTCGGCAAG

340       TTAGCATGACCCGACAGGTGGGCTTGGCTCGCGTAAGTTGAGTGTTGCAGATACCTGCTGCTGCGCGGTCTAGGGGGAATCGCCG
          AATCGTACTGGGCTGTCCACCCGAACCGAGCGCATTCAACTCACAACGTCTATGGACGACGACGCGCCAGATCCCCCTTAGCGGC

425       ATTTTGACGTAGGATCGGTAATGGGCAGTAAACCCGCAACTATTTTCAGCACCAGATGCAAGTTTCCCTAGAAAGCGTCATGGTT
          TAAAACTGCATCCTAGCCATTACCCGTCATTTGGGCGTTGATAAAAGTCGTGGTCTACGTTCAAAGGGATCTTTCGCAGTACCAA

510       TGCAATCTCCTTAGGTCACAGCAAACATAGCAGCCCCTGT
          ACGTTAGAGGAATCCAGTGTCGTTTGTATCGTCGGGGACA

Functions

`chunkify`(iterable, n)	Break an interable into chunks of size at most ‘n’
`indent`(string, indent)	Indent lines
`prepend_lines`(lines, label_iterable, indent)	Prepend lines with a label
`to_lines`(string, width)	Converts a string to lines of length <= width

Classes

`FASTAItem`(sequence)	SequenceViewer constructor
`FASTAViewer`(sequences)
`SequenceRow`(lines, labels, indent, start, end)	A row in a `SequenceViewer` instance.
`SequenceViewer`(sequences[, sequence_labels, …])	A class that views longs sets of sequences.
`StringColumn`([strings, color, background, fill])	Class for managing string columns
`ViewerAnnotationFlag`	Flags for annotation directions

class jdna.viewer.FASTAItem(sequence)[source]¶

Bases: jdna.viewer.SequenceViewer

SequenceViewer constructor

Parameters

sequences (list) – list of sequences to view
sequence_labels (list) – optional labels to apply to sequence. Include the ‘{index}’ to enumerate the base pairs.
foreground_colors (list) – optional list base pair foreground colors (hex or common name) to apply to each sequence. If a string is provided, color will be applied to all sequences. If provided with “RANDOM”, a random color will be assigned to each sequence.
background_colors (list) – optional list base pair background colors (hex or common name) to apply to each sequence. Usage is analogous to foreground_colors parameter.
indent (int) – spacing before start of string and start of base pairs
width (string) – width of the view window for the sequences (e.g. width=100 would mean rows of at most len 100 characters
spacer (string) – string to apply inbetween rows (default is newline)
name (basestring) – optional name for this viewer, to be displayed in the header
window (tuple) – tuple of the start and end points of the viewing window
description (basestring) – optional description for this viewer
metadata (dict) – optional metadata to display in the header

_annotate_rows(rows)¶: Annotate the rows using the viewer’s annotations

annotate(start, end, label=None, fill=None, color=None, background=None, top=True)¶

Annotates this viewer object starting from ‘start’ to ‘end’ inclusively.

Parameters

start (int) – inclusive start
end (int) – inclusive end
label (basestring | StringColumn) – optional label to apply to the annotation
fill (string) – the fill character to use to (e.g. ‘<’, ‘>’, ‘^’) to fill in whitespace
color (string) – the foreground color to apply to the annotation (hex or common name)
background (string) – the foreground color to apply to the annotation (hex or common name)

Returns

None

Return type

None

property header¶: Return the formatted header and metadata

set_window(start, end)¶: Sets the inclusive viewing window

class jdna.viewer.SequenceRow(lines, labels, indent, start, end, line_colors=None, line_backgrounds=None)[source]¶

Bases: object

A row in a SequenceViewer instance. Can be comprised of multiple sequences (i.e. lines) and can be annotated with ‘features’.

SequenceRow constructor

Parameters

lines (list) – list of lines to display. Lengths of all lines must all be equivalent.
labels (list) – list of labels to apply to each line
indent (string) – indent to apply to the lines
start (int) – start bp of this row
end (int) – end bp of this row

absolute_annotate(start, end, fill, label, color=None, background=None, top=True)[source]¶

Applyt annotation to this row using absolute start and ends for THIS row.

Parameters

start (int) – inclusive start
end (int) – inclusive end
fill (basestring) – what to fill whitespace with
label (basestring) – annotation label

Returns

None

Return type

None

annotate(start, end, fill, label='', color=None, background=None, top=True, wrap=False)[source]¶

Annotate the sequence row. If ‘start’ or ‘end’ is beyond, the expected start or end for this row, the annotation will automatically be truncated.

Parameters

start (int) – inclusive start
end (int) – inclusive end
fill – what to fill whitespace with
label (basestring) – optional label to apply to the annotation

Returns

Return type

in_bounds(x)[source]¶

Checks if the index ‘x’ is in between row start and end (inclusive)

Parameters: x (int) – index
Returns: if in bounds
Return type: bool

static make_annotation(label, span, fill='*', color=None, background=None)[source]¶

Make an annotation with ‘label’ spanning inclusive base pairs indices ‘span’

Parameters

label (basestring) – annotation label
span (tuple) – the start and end (inclusive) of the annotation
fill (basestring) – what to fill whitespace with

Returns

Return type

class jdna.viewer.SequenceViewer(sequences, sequence_labels=None, apply_indices=[0], foreground_colors=None, background_colors=None, indent=10, width=85, spacer='n', header_spacer='n', name='Unnamed', window=(0, None), description='', metadata=None)[source]¶

Bases: object

A class that views longs sets of sequences.

SequenceViewer constructor

Parameters

sequences (list) – list of sequences to view
sequence_labels (list) – optional labels to apply to sequence. Include the ‘{index}’ to enumerate the base pairs.
foreground_colors (list) – optional list base pair foreground colors (hex or common name) to apply to each sequence. If a string is provided, color will be applied to all sequences. If provided with “RANDOM”, a random color will be assigned to each sequence.
background_colors (list) – optional list base pair background colors (hex or common name) to apply to each sequence. Usage is analogous to foreground_colors parameter.
indent (int) – spacing before start of string and start of base pairs
width (string) – width of the view window for the sequences (e.g. width=100 would mean rows of at most len 100 characters
spacer (string) – string to apply inbetween rows (default is newline)
name (basestring) – optional name for this viewer, to be displayed in the header
window (tuple) – tuple of the start and end points of the viewing window
description (basestring) – optional description for this viewer
metadata (dict) – optional metadata to display in the header

_annotate_rows(rows)[source]¶: Annotate the rows using the viewer’s annotations

annotate(start, end, label=None, fill=None, color=None, background=None, top=True)[source]¶

Annotates this viewer object starting from ‘start’ to ‘end’ inclusively.

Parameters

start (int) – inclusive start
end (int) – inclusive end
label (basestring | StringColumn) – optional label to apply to the annotation
fill (string) – the fill character to use to (e.g. ‘<’, ‘>’, ‘^’) to fill in whitespace
color (string) – the foreground color to apply to the annotation (hex or common name)
background (string) – the foreground color to apply to the annotation (hex or common name)

Returns

None

Return type

None

property header¶: Return the formatted header and metadata

set_window(start, end)[source]¶: Sets the inclusive viewing window

class jdna.viewer.StringColumn(strings=None, color=None, background=None, fill=None)[source]¶

Bases: object

Class for managing string columns

StringColumn constructor.

Parameters: strings (list) – list of strings

classmethod condense(rows)[source]¶

Condense a list of StringColumn into the minimum number of StringColumns comprising of columns stripped of white space. Briefly, this is similar to the following procedure:

input = [
    'label         ',
    '       label2 ',
    '      label3  '
]

# >> CONDENSE

output = [
    'label  label2 ',
    '      label3  '
]

Parameters: rows –
Returns
Return type

classmethod string_length(string)[source]¶: String length, ignoring terminal formatting

class jdna.viewer.ViewerAnnotationFlag[source]¶

Bases: object

Flags for annotation directions

jdna.viewer.chunkify(iterable, n)[source]¶: Break an interable into chunks of size at most ‘n’

jdna.viewer.indent(string, indent)[source]¶: Indent lines

jdna.viewer.prepend_lines(lines, label_iterable, indent, fill=' ', align='<')[source]¶

Prepend lines with a label

Parameters

lines (list) – lines to prepend
indent (int) – number of spaces between start of label and start of line
fill (what to fill the spaces) – default ‘ ‘
align (string) – either left “<”, center “^” or right “>”

Returns

new prepended lines

Return type

list

jdna.viewer.to_lines(string, width)[source]¶: Converts a string to lines of length <= width

jdna

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jdna.viewer¶