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'])]