- BedTool.annotate(*args, **kwargs)¶
Annotate this BedTool with a list of other files. Example usage:
>>> a = pybedtools.example_bedtool('a.bed') >>> b_fn = pybedtools.example_filename('b.bed') >>> print(a.annotate(files=b_fn)) chr1 1 100 feature1 0 + 0.000000 chr1 100 200 feature2 0 + 0.450000 chr1 150 500 feature3 0 - 0.128571 chr1 900 950 feature4 0 + 0.020000
For convenience, the file or stream this BedTool points to is implicitly passed as the
Original BEDTools help::
Tool: bedtools annotate (aka annotateBed) Version: v2.31.0 Summary: Annotates the depth & breadth of coverage of features from mult. files on the intervals in -i. Usage: bedtools annotate [OPTIONS] -i <bed/gff/vcf> -files FILE1 FILE2..FILEn Options: -names A list of names (one / file) to describe each file in -i. These names will be printed as a header line. -counts Report the count of features in each file that overlap -i. - Default is to report the fraction of -i covered by each file. -both Report the counts followed by the % coverage. - Default is to report the fraction of -i covered by each file. -s Require same strandedness. That is, only counts overlaps on the **same** strand. - By default, overlaps are counted without respect to strand. -S Require different strandedness. That is, only count overlaps on the **opposite** strand. - By default, overlaps are counted without respect to strand.