pybedtools.bedtool.BedTool.closest

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

Wraps bedtools closest.

Return a new BedTool object containing closest features in b. Note that the resulting file is no longer a valid BED format; use the special “_closest” methods to work with the resulting file.

Example usage:

a = BedTool('in.bed')

# get the closest feature in 'other.bed' on the same strand
b = a.closest('other.bed', s=True)

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

Original BEDTools help::

Tool:    bedtools closest (aka closestBed)
Version: v2.30.0
Summary: For each feature in A, finds the closest 
         feature (upstream or downstream) in B.

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

Options: 
        -d      In addition to the closest feature in B, 
                report its distance to A as an extra column.
                - The reported distance for overlapping features will be 0.

        -D      Like -d, report the closest feature in B, and its distance to A
                as an extra column. Unlike -d, use negative distances to report
                upstream features.
                The options for defining which orientation is "upstream" are:
                - "ref"   Report distance with respect to the reference genome. 
                            B features with a lower (start, stop) are upstream
                - "a"     Report distance with respect to A.
                            When A is on the - strand, "upstream" means B has a
                            higher (start,stop).
                - "b"     Report distance with respect to B.
                            When B is on the - strand, "upstream" means A has a
                            higher (start,stop).

        -io     Ignore features in B that overlap A.  That is, we want close,
                yet not touching features only.

        -iu     Ignore features in B that are upstream of features in A.
                This option requires -D and follows its orientation
                rules for determining what is "upstream".

        -id     Ignore features in B that are downstream of features in A.
                This option requires -D and follows its orientation
                rules for determining what is "downstream".

        -fu     Choose first from features in B that are upstream of features in A.
                This option requires -D and follows its orientation
                rules for determining what is "upstream".

        -fd     Choose first from features in B that are downstream of features in A.
                This option requires -D and follows its orientation
                rules for determining what is "downstream".

        -t      How ties for closest feature are handled.  This occurs when two
                features in B have exactly the same "closeness" with A.
                By default, all such features in B are reported.
                Here are all the options:
                - "all"    Report all ties (default).
                - "first"  Report the first tie that occurred in the B file.
                - "last"   Report the last tie that occurred in the B file.

        -mdb    How multiple databases are resolved.
                - "each"    Report closest records for each database (default).
                - "all"  Report closest records among all databases.

        -k      Report the k closest hits. Default is 1. If tieMode = "all", 
                - all ties will still be reported.

        -N      Require that the query and the closest hit have different names.
                For BED, the 4th column is compared.

        -s      Require same strandedness.  That is, only report hits in B
                that overlap A on the **same** strand.
                - By default, overlaps are reported without respect to strand.

        -S      Require different strandedness.  That is, only report hits in B
                that overlap A on the **opposite** strand.
                - By default, overlaps are reported without respect to strand.

        -f      Minimum overlap required as a fraction of A.
                - Default is 1E-9 (i.e., 1bp).
                - FLOAT (e.g. 0.50)

        -F      Minimum overlap required as a fraction of B.
                - Default is 1E-9 (i.e., 1bp).
                - FLOAT (e.g. 0.50)

        -r      Require that the fraction overlap be reciprocal for A AND B.
                - In other words, if -f is 0.90 and -r is used, this requires
                  that B overlap 90% of A and A **also** overlaps 90% of B.

        -e      Require that the minimum fraction be satisfied for A OR B.
                - In other words, if -e is used with -f 0.90 and -F 0.10 this requires
                  that either 90% of A is covered OR 10% of  B is covered.
                  Without -e, both fractions would have to be satisfied.

        -split  Treat "split" BAM or BED12 entries as distinct BED intervals.

        -g      Provide a genome file to enforce consistent chromosome sort order
                across input files. Only applies when used with -sorted option.

        -nonamecheck    For sorted data, don't throw an error if the file has different naming conventions
                        for the same chromosome. ex. "chr1" vs "chr01".

        -names  When using multiple databases, provide an alias for each that
                will appear instead of a fileId when also printing the DB record.

        -filenames      When using multiple databases, show each complete filename
                        instead of a fileId when also printing the DB record.

        -sortout        When using multiple databases, sort the output DB hits
                        for each record.

        -bed    If using BAM input, write output as BED.

        -header Print the header from the A file prior to results.

        -nobuf  Disable buffered output. Using this option will cause each line
                of output to be printed as it is generated, rather than saved
                in a buffer. This will make printing large output files 
                noticeably slower, but can be useful in conjunction with
                other software tools and scripts that need to process one
                line of bedtools output at a time.

        -iobuf  Specify amount of memory to use for input buffer.
                Takes an integer argument. Optional suffixes K/M/G supported.
                Note: currently has no effect with compressed files.

Notes: 
        Reports "none" for chrom and "-1" for all other fields when a feature
        is not found in B on the same chromosome as the feature in A.
        E.g. none       -1      -1