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SangerTraces Documentation

SangerTraces is a package that allows users to visualize the contents of ab1 files. It comes with nine pre-made color schemes. The Hydrophobicity, HelixPropensity, StrandPropensity, TurnPropensity, and BuriedIndex color schemes were adapted from the pyMSAviz package.

Installation

pip install SangerTraces

Usage

Simple Usage

# Import the package
from sangertraces import SangerTrace

# Use the SangerTrace class to create the trace object
trace = SangerTrace(
    "B_reverse.ab1",
    start=10,
    end=100,
    wrap_length=80,
    translate=["FR1", "FR2", "FR3", "FR1_rev", "FR2_rev", "FR3_rev"],
    color_scheme="BuriedIndex"
)

# Call the plot_ab1_trace function to create a PIL image
fig2 = trace.plot_ab1_trace()

# Save the figure
fig2.save("Test1.png")

Parameters of the `SangerTrace` Class

filename (str, required) — Path to the AB1 file to visualize.
start (int, optional) — Start position for visualization (nucleotide number). Must be a positive integer. If an invalid value is provided, it defaults to 1.
end (int, optional) — End position for visualization. Must be a positive integer. If an invalid value is provided, it defaults to the full sequence length.
wrap_length (int, optional) — Number of bases to display per row. If not provided or an invalid value is provided, the entire sequence is displayed on one row. A wrap length of 60–120 is recommended for better readability.

translate (list or str, optional) — Translation frames for the sequence. If not provided, no translation is shown.

Accepts a list containing any of the following values: 'FR1', 'FR2', 'FR3', 'FR1_rev', 'FR2_rev', and 'FR3_rev'.

Alternatively, it accepts the string 'forward' (shows all forward frames) or 'reverse' (shows all reverse frames).

Using the reverse keyword. forward can be used in the same way.

from sangertraces import SangerTrace

trace = SangerTrace(
    "B_reverse.ab1",
    start=2,
    end=350,
    wrap_length=80,
    color_scheme="Simple",
    translate="reverse"
)

fig = trace.plot_ab1_trace()

# Save the figure
fig.save("Test2.png")

Using a list of values, e.g., ['FR1', 'FR2', 'FR3', 'FR1_rev', 'FR2_rev']:

from sangertraces import SangerTrace

trace = SangerTrace(
    "B_reverse.ab1",
    start=2,
    end=350,
    wrap_length=80,
    color_scheme="Simple",
    translate=["FR1", "FR2", "FR3", "FR1_rev", "FR2_rev"]
)

fig = trace.plot_ab1_trace()
fig.save("Test2.png")

color_scheme (str, optional) — Color scheme for nucleotide traces and translated proteins. Available options: 'Nazgul', 'Simple', 'ColorBlind', 'Geneious-like', 'Hydrophobicity', 'HelixPropensity', 'StrandPropensity', 'TurnPropensity', and 'BuriedIndex'. The default value is 'ColorBlind'.
The images below show how each color scheme looks:

BuriedIndex

ColorBlind

Geneious-like

HelixPropensity

Nazgul

Hydrophobicity

Simple

StrandPropensity

TurnPropensity
show_calls (bool, optional) — Whether to display base-call letters below the traces. The default is True. Set to False to disable.
show_quality (bool, optional) — Whether to display Phred quality scores as bars. The default is True. Set to False to disable.
plot_title (str, optional) — plot title.