API reference

class overhang.Overhang(seq)

Class for an overhang and its reverse complement.

Note that the overhang with the lower order (e.g., AATA < TATT) will be stored in Overhang.overhang and the reverse complement in Overhang.overhang_rc, regardless of which was given as parameter.

Parameters:

seq (str) – ACGT sequence.

count_max_repeat(repeat=3)

Check overhang for repeating letters.

Parameters:

repeat (int) – Number of minimum repeats to flag. For example, 3 checks for AAA etc.

find_codons()

Check overhang for presence of start and stop codons.

This is important information on the suitability of an overhang.

is_good()

Summarise attributes and decide whether overhang can be used for assembly.

class overhang.generate_all_overhangs(overhang_length=4)

Generate list of Overhang class instances for all overhangs of given length.

Parameters:

overhang_length (int) – Length of overhangs.

class overhang.OverhangSet(overhangs, enzyme='Esp3I', name='Unnamed set')

Class for overhang sets.

An overhang set is a collection of (mutually compatible) overhangs used for DNA assembly.

Parameters:

  • overhangs (list of str) – A list of overhang strings. Example: [“TAGG”, “ATGG”, “GACT”].

  • enzyme (str) – Enzyme used for assembly. Example: “Esp3I”.

  • name (str) – Name of the set.

evaluate_annealing()

Evaluate weak anneals, self-misanneals and misanneals between overhangs.

Used in inspect_overhangs().

find_perfect_subset()

Find a better overhang set by removing bad overhang interactions.

Bad interactions are weak anneals, self-misanneals and misanneals.

find_similar_overhangs(difference_threshold=None)

Find overhangs that differ in fewer nucleotides than the threshold.

Parameters:

difference_threshold (int) – Acceptable number of matching nucleotides in an overhang pair. Overhang pairs with fewer differences are marked as similar. Defaults to 0.

inspect_overhangs(make_plot=True)

Inspect compatibility of overhangs and detect potential errors in the set.

class overhang.order_overhangs(seq)

Create an overhang’s reverse complement, and return them in order.

Overhangs are ordered by the letters, e.g., AATA < TATT.

Parameters:

seq (str) – ACGT sequence.

class overhang.generate_overhang_pairs(overhang_length=4)

Generate all overhang pairs of given length.

Parameters:

overhang_length (int) – Length of overhangs.

class overhang.subset_data_for_overhang(dataframe, overhang, horizontal=True, filter=True)

Subset Tatapov dataframe for given overhang.

Parameters:

  • dataframe (DataFrame) – Tatapov dataset, for example tatapov.annealing_data[“25C”][“01h”].

  • overhang (Overhang) – Overhang class instance.

  • horizontal (bool) – Orientation of returned dataframe.

  • filter (bool) – If True, keep only columns (if horizontal=True) or rows (if horizontal=False) with nonzero values.

class overhang.plot_data(df, ax=None, colorbar=True, figwidth=8, plot_color='Reds')

Plot a (restricted) Tatapov dataframe.

Parameters:

  • df (DataFrame) – One of the data sheets provided by tatapov, e.g. annealing_data[“37C”][“01h”]. Or a restriction using data_subset.

  • ax (matplotlib.axes.Axes, optional) – A Matplotlib ax. If none is provided, one will be created and returned at the end.

  • colorbar (bool) – If True, the figure will have a colorbar.

  • figwidth (float, optional) – Custom width of the figure.

  • plot_color (str) – A Matplotlib colormap name.

class overhang.filter_overhangs(overhangs, enzyme='Esp3I')

Filter overhangs using the Tatapov package.

Filter out the weakly annealing and self-misannealing overhangs.

Parameters:

  • overhangs (list of Overhang) – List of Overhang instances.

  • enzyme (str) – Enzyme used with the overhangs. See overhang.tools.enzyme_tatapov_lookup for options.

class overhang.write_pdf_report(target, overhangs, enzyme='Esp3I')

Write an overhang compendium.

Parameters:

  • target (str) – Path for PDF file.

  • overhangs (list of Overhang) – List of Overhang instances.

  • enzyme (str) – Enzyme used for assembly. Options: “BsaI”, “BsmBI”, “Esp3I”, or “BbsI”.

class overhang.write_overhangset_report(target, overhangset)

Write a report on an overhang set.

Parameters:

  • target (str) – Path for PDF file.

  • overhangset (OverhangSet) – An OverhangSet instance.