pybedtools.bedtool.BedTool.slop

BedTool.slop(*args, **kwargs)

Wraps bedtools slop.

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

There are two alternatives for supplying a genome. Use g="genome.filename" if you have a genome’s chrom sizes saved as a file. This is the what BEDTools expects when using it from the command line. Alternatively, use the genome="assembly.name" (for example, genome="hg19") to use chrom sizes for that assembly without having to manage a separate file. The genome argument triggers a call pybedtools.chromsizes, so see that method for more details.

Original BEDTools help::

Tool:    bedtools slop (aka slopBed)
Version: v2.31.1
Summary: Add requested base pairs of "slop" to each feature.

Usage:   bedtools slop [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]

Options: 
        -b      Increase the BED/GFF/VCF entry -b base pairs in each direction.
                - (Integer) or (Float, e.g. 0.1) if used with -pct.

        -l      The number of base pairs to subtract from the start coordinate.
                - (Integer) or (Float, e.g. 0.1) if used with -pct.

        -r      The number of base pairs to add to the end coordinate.
                - (Integer) or (Float, e.g. 0.1) if used with -pct.

        -s      Define -l and -r based on strand.
                E.g. if used, -l 500 for a negative-stranded feature, 
                it will add 500 bp downstream.  Default = false.

        -pct    Define -l and -r as a fraction of the feature's length.
                E.g. if used on a 1000bp feature, -l 0.50, 
                will add 500 bp "upstream".  Default = false.

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

Notes: 
        (1)  Starts will be set to 0 if options would force it below 0.
        (2)  Ends will be set to the chromosome length if requested slop would
        force it above the max chrom length.
        (3)  The genome file should be tab delimited and structured as follows:

        <chromName><TAB><chromSize>

        For example, Human (hg19):
        chr1    249250621
        chr2    243199373
        ...
        chr18**gl000207**random 4262

Tip 1. Use samtools faidx to create a genome file from a FASTA: 
        One can the samtools faidx command to index a FASTA file.
        The resulting .fai index is suitable as a genome file, 
        as bedtools will only look at the first two, relevant columns
        of the .fai file.

        For example:
        samtools faidx GRCh38.fa
        bedtools slop -b 10 -i my.bed -g GRCh38.fa.fai

Tip 2. Use UCSC Table Browser to create a genome file: 
        One can use the UCSC Genome Browser's MySQL database to extract
        chromosome sizes. For example, H. sapiens:

        mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
        "select chrom, size from hg19.chromInfo"  > hg19.genome