# pybedtools.bedtool.BedTool.complement

BedTool.complement(*args, **kwargs)

  > Wraps `bedtools complement`. Example usage:

  >     >>> a = pybedtools.example_bedtool('a.bed')
  >     >>> a.complement(genome='hg19').head(5)
  >     chr1    0       1
  >     chr1    500     900
  >     chr1    950     249250621
  >     chr2    0       243199373
  >     chr3    0       198022430

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

  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 complement (aka complementBed)
      Version: v2.31.1
      Summary: Returns the base pair complement of a feature file.

      Usage:   bedtools complement [OPTIONS] -i <bed/gff/vcf> -g <genome>

      Options:
              -L      Limit output to solely the chromosomes with records in the input file.

      Notes:
              (1)  The genome file should 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 complement -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