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Commit 54cf991e authored by Aaron's avatar Aaron
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[DOCS] update maskfasta docs

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docs/content/tools/maskfasta.rst
+ 63
− 25
View file @ 54cf991e
###############
*maskfasta*
###############
**maskFastaFromBed** masks sequences in a FASTA file based on intervals defined in a feature file. The
|
.. image:: ../images/tool-glyphs/maskfasta-glyph.png
:width: 600pt
``bedtools maskfasta`` masks sequences in a FASTA file based on intervals defined in a feature file. The
headers in the input FASTA file must exactly match the chromosome column in the feature file. This
may be useful fro creating your own masked genome file based on custom annotations or for masking all
but your target regions when aligning sequence data from a targeted capture experiment.
......@@ -10,61 +18,91 @@ but your target regions when aligning sequence data from a targeted capture expe
==========================================================================
Usage and option summary
==========================================================================
Usage:
::
maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
**Usage**
.. code-block:: bash
$ bedtools maskfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
NOTE: The input and output FASTA files must be different.
**(or):**
.. code-block:: bash
$ maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-soft** Soft-mask (that is, convert to lower-case bases) the FASTA sequence. *By default, hard-masking (that is, conversion to Ns) is performed*.
=========================== ===============================================================================================================================================================================================================
.. note::
The input (``-fi``) and output (``-fo``) FASTA files must be different.
=========================== ==========================================================================================================================================
Option Description
=========================== ==========================================================================================================================================
**-soft** Soft-mask (that is, convert to lower-case bases) the FASTA sequence. *By default, hard-masking (that is, conversion to Ns) is performed*.
**-mc** Replace masking character. That is, instead of masking with Ns, use another character.
=========================== ==========================================================================================================================================
==========================================================================
Default behavior
==========================================================================
**maskFastaFromBed** will mask a FASTA file based on the intervals in a BED file. The newly masked
FASTA file is written to the output FASTA file.
**bedtools maskfasta** will mask a FASTA file based on the intervals in a
BED file. The newly masked FASTA file is written to the output FASTA file.
.. code-block:: bash
For example:
::
cat test.fa
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
cat test.bed
$ cat test.bed
chr1 5 10
maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out
$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out
cat test.fa.out
$ cat test.fa.out
>chr1
AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
==========================================================================
Soft-masking the FASTA file.
``-soft`` Soft-masking the FASTA file.
==========================================================================
Using the **-soft** option, one can optionally "soft-mask" the FASTA file.
For example:
::
cat test.fa
.. code-block:: bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
cat test.bed
$ cat test.bed
chr1 5 10
maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out -soft
$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -soft
cat test.fa.out
$ cat test.fa.out
>chr1
AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
==========================================================================
``-mc`` Specify a masking character.
==========================================================================
Using the **-mc** option, one can optionally choose a masking character to each
base that will be masked by the BED file.
.. code-block:: bash
$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
$ cat test.bed
chr1 5 10
$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -mc X
$ cat test.fa.out
>chr1
AAAAAXXXXXCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
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