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

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: v2.30.0
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 and coordinates for the FASTA header
        -name+          (deprecated) Use the name field and coordinates for the FASTA header
        -nameOnly       Use the name field 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.
        -bedOut         Report extract sequences in a tab-delimited BED format instead of in FASTA 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.
        -rna    The FASTA is RNA not DNA. Reverse complementation handled accordingly.