pybedtools.bedtool.BedTool.pair_to_bed

BedTool.pair_to_bed(*args, **kwargs)[source]

Wraps bedtools pairtobed.

For convenience, the file or stream this BedTool points to is implicitly passed as the -a argument to pairToBed

Original BEDTools help::

Tool:    bedtools pairtobed (aka pairToBed)
Version: v2.30.0
Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file.

Usage:   bedtools pairtobed [OPTIONS] -a <bedpe> -b <bed/gff/vcf>

Options: 
        -abam   The A input file is in BAM format.  Output will be BAM as well. Replaces -a.
                - Requires BAM to be grouped or sorted by query.

        -ubam   Write uncompressed BAM output. Default writes compressed BAM.

                is to write output in BAM when using -abam.

        -bedpe  When using BAM input (-abam), write output as BEDPE. The default
                is to write output in BAM when using -abam.

        -ed     Use BAM total edit distance (NM tag) for BEDPE score.
                - Default for BEDPE is to use the minimum of
                  of the two mapping qualities for the pair.
                - When -ed is used the total edit distance
                  from the two mates is reported as the score.

        -f      Minimum overlap required as fraction of A (e.g. 0.05).
                Default is 1E-9 (effectively 1bp).

        -s      Require same strandedness when finding overlaps.
                Default is to ignore stand.
                Not applicable with -type inspan or -type outspan.

        -S      Require different strandedness when finding overlaps.
                Default is to ignore stand.
                Not applicable with -type inspan or -type outspan.

        -type   Approach to reporting overlaps between BEDPE and BED.

                either  Report overlaps if either end of A overlaps B.
                        - Default.
                neither Report A if neither end of A overlaps B.
                both    Report overlaps if both ends of A overlap  B.
                xor     Report overlaps if one and only one end of A overlaps B.
                notboth Report overlaps if neither end or one and only one 
                        end of A overlap B.  That is, xor + neither.

                ispan   Report overlaps between [end1, start2] of A and B.
                        - Note: If chrom1 <> chrom2, entry is ignored.

                ospan   Report overlaps between [start1, end2] of A and B.
                        - Note: If chrom1 <> chrom2, entry is ignored.

                notispan        Report A if ispan of A doesn't overlap B.
                                - Note: If chrom1 <> chrom2, entry is ignored.

                notospan        Report A if ospan of A doesn't overlap B.
                                - Note: If chrom1 <> chrom2, entry is ignored.

Refer to the BEDTools manual for BEDPE format.