pybedtools.bedtool.BedTool.sequence

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

Wraps bedtools getfasta.

fi is passed in by the user; bed is automatically passed in as the bedfile of this object; fo by default is a temp file. Use save_seqs() to save as a file.

The end result is that this BedTool will have an attribute, self.seqfn, that points to the new fasta file.

Example usage:

>>> a = pybedtools.BedTool("""
... chr1 1 10
... chr1 50 55""", from_string=True)
>>> fasta = pybedtools.example_filename('test.fa')
>>> a = a.sequence(fi=fasta)
>>> print(open(a.seqfn).read())
>chr1:1-10
GATGAGTCT
>chr1:50-55
CCATC
<BLANKLINE>

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

Original BEDTools help::

Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.27.1
Summary: Extract DNA sequences from a fasta file based on feature coordinates.

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

Options: 
        -fi     Input FASTA file
        -fo     Output file (opt., default is STDOUT
        -bed    BED/GFF/VCF file of ranges to extract from -fi
        -name   Use the name field for the FASTA header
        -name+  Use the name field and coordinates for the FASTA header
        -split  given BED12 fmt., extract and concatenate the sequences
                from the BED "blocks" (e.g., exons)
        -tab    Write output in TAB delimited format.
                - Default is FASTA format.

        -s      Force strandedness. If the feature occupies the antisense,
                strand, the sequence will be reverse complemented.
                - By default, strand information is ignored.

        -fullHeader     Use full fasta header.
                - By default, only the word before the first space or tab 
                is used.