diff --git a/src/isotools/_transcriptome_io.py b/src/isotools/_transcriptome_io.py index 26fcebd..1c95d62 100644 --- a/src/isotools/_transcriptome_io.py +++ b/src/isotools/_transcriptome_io.py @@ -2238,12 +2238,12 @@ def aligned_part(cigartuples, is_reverse): return (start, end) end += cigar[1] start = end - return (start, end) # clipping at begining or no clipping + return (start, end) # clipping at beginning or no clipping def get_clipping(cigartuples, pos): if cigartuples[0][0] == 4: - # clipping at the begining + # clipping at the beginning return (pos, -cigartuples[0][1]) elif cigartuples[-1][0] == 4: # clipping at the end - get the reference position diff --git a/src/isotools/_utils.py b/src/isotools/_utils.py index b0b00ce..c23ef88 100644 --- a/src/isotools/_utils.py +++ b/src/isotools/_utils.py @@ -132,7 +132,7 @@ def basequal_hist(bam_fn, qual_bins=None, len_bins=None, n=10000): return pd.DataFrame(qual, index=idx, columns=col) -def pairwise(iterable): # e.g. usefull for enumerating introns +def pairwise(iterable): # e.g. useful for enumerating introns "s -> (s0,s1), (s1,s2), (s2, s3), ..." a, b = itertools.tee(iterable) next(b, None) diff --git a/src/isotools/plots.py b/src/isotools/plots.py index 5f01c42..8c0a248 100644 --- a/src/isotools/plots.py +++ b/src/isotools/plots.py @@ -118,7 +118,7 @@ def plot_diff_results( "vs".join(str(p[0]) for p in params_alt.values()), ) continue - # get the paramters for the beta distiribution + # get the parameters for the beta distribution ax = axs[len(plotted)] # ax.boxplot([mut,wt], labels=['mut','wt']) sns.swarmplot( @@ -180,7 +180,7 @@ def plot_embedding( :param top_var: Number of alternative splicing events which are used for the embedding. :param min_total: Minimum total coverage over all selected samples. :param min_alt_fraction: Minimum fraction of reads supporting the alternative (for both groups combined). - :param plot_components: The dimentions to plot (E.g. the components of the PCA) + :param plot_components: The dimensions to plot (E.g. the components of the PCA) :param splice_types: Restrict the analysis on specified splicing event(s). :param labels: If True, sample names are printed in the plot next to the corresponding points. :param groups: Set a group definition (e.g. by isoseq.Transcirptome.groups()) to color the datapoints. diff --git a/src/isotools/splice_graph.py b/src/isotools/splice_graph.py index 58056b6..71d3945 100755 --- a/src/isotools/splice_graph.py +++ b/src/isotools/splice_graph.py @@ -415,7 +415,7 @@ def get_alternative_splicing(self, exons: list[tuple[int, int]], alternative=Non ) # j2: index of last segment starting before exon end (i.e. last overlapping segment) - # check truncation at begining (e.g. low position) + # check truncation at beginning (e.g. low position) if ( len(exons) > 1 # no mono exon and not any(