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Compatibility with biopython 1.8.0 and bokeh 3 #74

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Dec 17, 2022
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Compatibility with biopython 1.8.0 and bokeh 3 #74

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4 changes: 2 additions & 2 deletions dna_features_viewer/GraphicRecord/BokehPlottableMixin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,8 +92,8 @@ def plot_with_bokeh(self, figure_width=5, figure_height="auto", tools="auto"):

# BUILD THE PLOT ()
plot = figure(
plot_width=width,
plot_height=height,
width=width,
height=height,
tools=tools,
x_range=Range1d(0, self.sequence_length),
y_range=Range1d(-1, max_y + 1),
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16 changes: 12 additions & 4 deletions dna_features_viewer/biotools.py
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Expand Up @@ -34,9 +34,17 @@ def reverse_complement(sequence):
return complement(sequence)[::-1]


aa_short_to_long_form_dict = {
_aa1: _aa3[0] + _aa3[1:].lower() for (_aa1, _aa3) in zip(aa1 + "*", aa3 + ["*"])
}
if type(aa1) is str and type(aa3) is list:
# biopython before 1.8.0
aa_short_to_long_form_dict = {
_aa1: _aa3[0] + _aa3[1:].lower() for (_aa1, _aa3) in zip(aa1 + "*", aa3 + ["*"])
}
else:
# biopython 1.8.0 and later
# relevant commit: https://github.com/biopython/biopython/commit/257143be9196b77619d3d8cadc22039212681e08
aa_short_to_long_form_dict = {
_aa1: _aa3[0] + _aa3[1:].lower() for (_aa1, _aa3) in zip(aa1 + ('*',), aa3 + ('*',))
}


def translate(dna_sequence, long_form=False):
Expand Down Expand Up @@ -123,7 +131,7 @@ def load_record(path, filetype=None):


def annotate_biopython_record(
seqrecord, location="full", feature_type="misc_feature", margin=0, **qualifiers
seqrecord, location="full", feature_type="misc_feature", margin=0, **qualifiers
):
"""Add a feature to a Biopython SeqRecord.

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