API reference

class crazydoc.StyleObserver

Generic class for observing style-based annotations in sequences.

The provided subclasses each observe one particular type of DNA sequence annotation, such as the highlight color, bold text, underlines, etc.

class crazydoc.CrazydocParser(observers)

Parser to translate MS Word docx documents to Biopython records.

Parameters:: observers (list) – A list of either crazydoc.Observer objects or observer names in highlight_color, font_color, bold, italic, upper_case, lower_case, underline.

Examples

>>> parser = CrazydocParser(['highlight_color', 'font_color'])
>>> biopython_records = parser.parse_doc_file('example.docx')

parse_doc_file(filepath=None, doc=None, is_protein=False)

Return a list of records, 1 for each sequence contained in the docx.

Parameters:

filepath (str, optional) – A path to a docx file.
doc (Document, optional) – A python-docx Document object, which can be provided instead of the file path.
is_protein (bool, optional) – True if the sequences are protein sequences (default: False).

class crazydoc.CrazydocSketcher

Unavailable class: install DnaFeaturesViewer.

Try: pip install dna_features_viewer

crazydoc.write_crazydoc(seqs, qualifier, path, formats=[[WD_COLOR_INDEX.GREEN, WD_COLOR_INDEX.GRAY_25, WD_COLOR_INDEX.TEAL, WD_COLOR_INDEX.VIOLET, WD_COLOR_INDEX.RED, WD_COLOR_INDEX.GRAY_50, WD_COLOR_INDEX.DARK_YELLOW, WD_COLOR_INDEX.DARK_RED, WD_COLOR_INDEX.DARK_BLUE], [(248, 118, 109), (183, 159, 0), (0, 186, 56), (0, 191, 196), (97, 156, 255), (245, 100, 227)], ['bold'], ['underline'], ['italic']])

Write one or more SeqRecords annotated with features to a new document.

WILL OVERWRITE EXISTING DOCUMENTS WITHOUT WARNING!

Parameters:

seqs (list) – List of SeqRecords to write out.
qualifier (str) – The key to use for feature names from .qualifiers.
path (str) – The path to write the document to. Will overwrite existing documents!
formats (list, optional) – List of format groups to use on features.

Examples

A custom list of docx formats can be supplied to the formats argument. If formats is not declared a default palette is used.

>>> from docx.shared import RGBColor
>>> from docx.enum.text import WD_COLOR
>>> custom_formats = [
        [
            WD_COLOR.PINK,
            WD_COLOR.TEAL,
            WD_COLOR.YELLOW,
            WD_COLOR.GRAY_50,
            WD_COLOR.VIOLET,
            WD_COLOR.TURQUOISE,
        ],
        [
            RGBColor(0xFF, 0x00, 0x00),
            RGBColor(0x00, 0xFF, 0x00),
            RGBColor(0x00, 0x00, 0xFF),
        ],
        ["bold"],
        ["underline"],
        ["italic"],
    ]
>>> write_crazydoc(seq, 'product', 'custom_colours.docx', formats=custom_formats)

crazydoc.write_crazyseq(seqrec, qualifier, doc, formats=[[WD_COLOR_INDEX.GREEN, WD_COLOR_INDEX.GRAY_25, WD_COLOR_INDEX.TEAL, WD_COLOR_INDEX.VIOLET, WD_COLOR_INDEX.RED, WD_COLOR_INDEX.GRAY_50, WD_COLOR_INDEX.DARK_YELLOW, WD_COLOR_INDEX.DARK_RED, WD_COLOR_INDEX.DARK_BLUE], [(248, 118, 109), (183, 159, 0), (0, 186, 56), (0, 191, 196), (97, 156, 255), (245, 100, 227)], ['bold'], ['underline'], ['italic']])

Write a single sequence with annotated features to an existing document element. If you want crazydoc to handle document creation, use write_crazydoc() even for single sequences.

Parameters:

seqrec (SeqRecord) – The sequence to write, with features.
qualifier (str) – The key of the .qualifier to use as feature names.
doc (docx document) – The docx document element to write to.
formats (list, optional) – List of format groups to use on features.

crazydoc.make_groups(position_features)

Make groups where no overlapping features share a group.

Parameters:: position_features (list of lists) – Each sublist represents a single position in the sequence and lists all the features that position is part of.
Returns:: Each sublist contains all features in a single group. Groups can use a single type of formatting, e.g., highlighting or font color.
Return type:: list of lists

crazydoc.records_to_genbank(records, path='.', extension=None, is_protein=False)