How do I

Obtain overlapping intervals with matching strandedness?

Use overlap with the on argument:

df = bf.overlap(df1, df2, on=[‘strand’])

Obtain overlapping intervals with opposite strandedness?

Overlap then filter pairs of opposite strandedness:

df = bf.overlap(df1, df2)
df = df.loc[df["strand"]!=df["strand_"]]

Obtain intervals that exceed 50% coverage by another set of intervals?

Coverage, then filter pairs by fractional coverage:

df = bf.coverage(df1, df2)
df = df[ ( df["coverage"] / (df["end"]-df["start"]) ) >=0.50]

Shift all intervals on the positive strand by 10bp?

Use pandas indexing:

df.loc[df.strand=="+",["start", "end"]] += 10

Obtain intervals overlapped by at least 2 intervals from another set?

Count overlaps, then filter:

df = bf.count_overlaps(df1, df2)
df = df[ df["count"] >= 2]

Find strand-specific downstream genomic features?

Use closest after filtering by strand, and passing the ignore_upsream=True argument.

bioframe.closest(df1.loc[df1['strand']=='+'], df2, ignore_upstream=True)

For gener, the upstream/downstream direction might be defined by the direction of transcription. Use direction_col='strand' to set up the direction:

bioframe.closest(df1, df2, ignore_upstream=True, direction_col='strand')

Drop non-autosomes from a bedframe?

Use pandas DataFrame.isin(values):

df[ ~df.chrom.isin(['chrX','chrY'])]