pybedtools.bedtool.BedTool.mask_fasta

BedTool.mask_fasta(*args, **kwargs)

Wraps bedtools maskfasta.

Masks a fasta file at the positions in a BED file and saves result as ‘out’ and stores the filename in seqfn.

>>> a = pybedtools.BedTool('chr1 100 110', from_string=True)
>>> fasta_fn = pybedtools.example_filename('test.fa')
>>> a = a.mask_fasta(fi=fasta_fn, fo='masked.fa.example')
>>> b = a.slop(b=2, genome='hg19')
>>> b = b.sequence(fi=a.seqfn)
>>> print(open(b.seqfn).read())
>chr1:98-112
TTNNNNNNNNNNAT

>>> os.unlink('masked.fa.example')
>>> if os.path.exists('masked.fa.example.fai'):
...     os.unlink('masked.fa.example.fai')

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

Original BEDTools help::

Tool:    bedtools maskfasta (aka maskFastaFromBed)
Version: v2.31.1
Summary: Mask a fasta file based on feature coordinates.

Usage:   bedtools maskfasta [OPTIONS] -fi <fasta> -fo <fasta> -bed <bed/gff/vcf>

Options:
        -fi             Input FASTA file
        -bed            BED/GFF/VCF file of ranges to mask in -fi
        -fo             Output FASTA file
        -soft           Enforce "soft" masking.
                        Mask with lower-case bases, instead of masking with Ns.
        -mc             Replace masking character.
                        Use another character, instead of masking with Ns.
        -fullHeader     Use full fasta header.
                        By default, only the word before the first space or tab
                        is used.