bedtools----getfasta

bedtools getfasta extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.

getfasta可以根据BED/GFF/VCF文件提供的feature在染色体上的位置信息，从fasta中提取feature的碱基序列

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

Tip

1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.#FASTA 中序列名与BED文件中染色体名字要一一对应，不然找不到；类似于perl中hash,python中字典。
2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
3. BED files containing a single region require a newline character at the end of the line, otherwise a blank output file is produced.

$ bedtools getfasta -h

Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.25.0
Summary: Extract DNA sequences into a fasta file based on feature coordinates.

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

Options:
-fi     Input FASTA file #samtools先建立index再使用
-bed    BED/GFF/VCF file of ranges to extract from -fi
-fo     Output file(can be FASTA or TAB-delimited)
-name   Use the name field for the FASTA header
-split  given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
-tab    Write output in TAB delimited format.#格式：name \t sequence
                - 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.#考虑链的正负方向，+提取正链序列，-提取正链序列

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

例子：

结果文件中fasta格式序列名字默认格式： “<chrom>:<start>-<end>”。-name可设定提取的序列名字为对应的BED文件中feature名字

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools getfasta -fi test.fa -bed test.bed
>chr1:5-10
AAACC

# optionally write to an output file
$ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out

$ cat test.fa.out
>chr1:5-10
AAACC
#-name设定提取的序列名字为对应的BED文件中feature名字
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10 myseq

$ bedtools getfasta -fi test.fa -bed test.bed -name
>myseq
AAACC

-s #考虑链的正负方向，+提取正链序列，-提取正链序列

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 20 25 forward 1 +
chr1 20 25 reverse 1 -

$ bedtools getfasta -fi test.fa -bed test.bed -s -name
>forward
CGCTA
>reverse
TAGCG