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.. _getfasta:
###############
*getfasta*
###############
|
.. image:: ../images/tool-glyphs/getfasta-glyph.png
:width: 600pt
``bedtools getfasta`` extracts sequences from a FASTA file for each of the
intervals defined in a BED/GFF/VCF file.
.. tip::
1. The headers in the input FASTA file must *exactly* match the chromosome
column in the BED file.
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.
.. seealso::
:doc:`../tools/maskfasta`
==========================================================================
Usage and option summary
==========================================================================
**Usage**
.. code-block:: bash
$ bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>
**(or):**
.. code-block:: bash
$ getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-fo** Specify an output file name. By default, output goes to stdout.
**-name** Use the "name" column in the BED file for the FASTA headers in the output FASTA file.
**-tab** Report extract sequences in a tab-delimited format instead of in FASTA format.
**-bedOut** Report extract sequences in a tab-delimited BED format instead of in FASTA format.
**-s** Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. *Default: strand information is ignored*.
**-split** Given BED12 input, extract and concatenate the sequences from the BED "blocks" (e.g., exons)
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
``bedtools getfasta`` will extract the sequence defined by the coordinates
in a BED interval and create a new FASTA entry in the output file for each
extracted sequence. By default, the FASTA header for each
extracted sequence will be formatted as follows: "<chrom>:<start>-<end>".
.. code-block:: bash
$ 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`` Using the BED "name" column as a FASTA header.
==========================================================================
Using the ``-name`` option, one can set the FASTA header for each extracted
sequence to be the "name" columns from the BED feature.
.. code-block:: bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
$ cat test.bed
chr1 5 10 myseq
$ bedtools getfasta -fi test.fa -bed test.bed -name
>myseq
AAACC
==========================================================================
``-tab`` Creating a tab-delimited output file in lieu of FASTA output.
==========================================================================
Using the ``-tab`` option, the ``-fo`` output file will be tab-delimited
instead of in FASTA format.
.. code-block:: bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
$ cat test.bed
chr1 5 10 myseq
$ bedtools getfasta -fi test.fa -bed test.bed -name -tab
myseq AAACC
==========================================================================
``-bedOut`` Creating a tab-delimited BED file in lieu of FASTA output.
==========================================================================
Using the ``-tab`` option, the ``-fo`` output file will be tab-delimited
instead of in FASTA format.
.. code-block:: bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
$ cat test.bed
chr1 5 10 myseq
$ bedtools getfasta -fi test.fa -bed test.bed -tab
chr1 5 10 AAACC
==========================================================================
``-s`` Forcing the extracted sequence to reflect the requested strand
==========================================================================
``bedtools getfasta`` will extract the sequence in the orientation defined in
the strand column when the "-s" option is used.
.. code-block:: bash
$ 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
==========================================================================
``-split`` Extracting BED "blocks".
==========================================================================
One can optionally request that FASTA records be extracting and concatenating
each block in a BED12 record. For example, consider a BED12 record describing a
transcript. By default, ``getfasta`` will extract the sequence representing the
entire transcript (intons, exons, UTRs). Using the -split option, ``getfasta``
will instead produce separate a FASTA record representing a transcript that
splices together each BED12 block (e.g., exons
and UTRs in the case of genes described with BED12).
.. code-block:: bash
$ cat genes.bed12
chr1 164404 173864 ENST00000466557.1 0 - 173864 173864 0 6 387,59,66,216,132,112, 0,1479,3695,4644,8152,9348,
chr1 235855 267253 ENST00000424587.1 0 - 267253 267253 0 4 2100,150,105,158, 0,2562,23161,31240,
chr1 317810 328455 ENST00000426316.1 0 + 328455 328455 0 2 323,145, 0,10500,
$ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name
>ENST00000466557.1
gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattagcctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagcctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtgatggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggcagcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcctcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggccttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGTCCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctcctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGCAGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAATAATCATCATCT
>ENST00000424587.1
ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggattacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGTAAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtccatctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgccctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGCATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAAGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggccgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagccccagctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtgagccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaaaaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAAGCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTACAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTTTGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactcttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCAAAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG
>ENST00000426316.1
AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgagagaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtatgagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGCAAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTTTGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTTGTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTTCCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATATTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA
# use the UNIX fold command to wrap the FASTA sequence such that each line
# has at most 60 characters
$ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name | \
fold -w 60
>ENST00000466557.1
gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggag
ttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattag
cctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatt
tcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagc
ctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGG
GAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCA
CCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTT
CACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTT
ACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtg
atggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggca
gcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcc
tcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggc
cttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGT
CCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctc
ctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGC
AGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAA
TAATCATCATCT
>ENST00000424587.1
ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggat
tacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGG
CTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGT
AAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTC
TGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTT
TATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGG
GTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGT
TTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATT
TGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACA
TAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtcc
atctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatatta
acaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgc
cctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGA
CAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGAC
AGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACA
GTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagacc
agcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaat
aagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATA
CTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGC
ATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCT
CGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGA
GGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCA
GCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAA
AGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggc
cgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaacc
ccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagcccc
agctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtg
agccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaa
aaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAA
GCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTT
CCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAA
GGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCA
GCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTA
CAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTT
TGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaact
cttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgt
gcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagtt
ctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCT
CTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTC
TTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCA
AAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTC
ATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG
>ENST00000426316.1
AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgag
agaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtat
gagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGC
AAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTT
TGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTT
GTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTT
CCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATA
TTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA
|
