setSequence
Update read sequences
Syntax
Description
returns a new object that is a copy of newObject
= setSequence(object
,sequenceInfo
)object
with the
Sequence
property set to
sequenceInfo
.
returns a new object that is a copy of newObject
= setSequence(object
,sequenceInfo
,subset
)object
with the
Sequence
property of a subset of elements set to
sequenceInfo
. A one-to-one relationship must exist between
the number and order of elements in sequenceInfo
and
subset
.
Examples
Update Read Sequences
Store read data from a SAM-formatted file in a BioRead object. Set 'InMemory'
to true
to load the object into memory so that you can modify its properties.
br = BioRead('SRR005164_1_50.fastq','InMemory',true)
br = BioRead with properties: Quality: {50x1 cell} Sequence: {50x1 cell} Header: {50x1 cell} NSeqs: 50 Name: ''
Check the read sequences of the first three elements of the object.
br.Sequence(1:3)
ans = 3x1 cell
{'TGGCTTTAAAGCAGAACTTGTGAAAGAAGGAAAGCATTATGATTATCTGGCTAAGCTTAGCATTGTTTAGAA' }
{'TTACACTATCCTCTGATTACCAAAGACGTTTCTCGGTCATACAGACAGTCCTTGAGCAAGGGAAGAATTTATTTGCAGGCAAAAAAGTGTCCAACCGTATCGTGAGTATCGACCGGCATTACCTT' }
{'CACGAGCGGTATATTTGCCTTTTTGTGCTGTGATTCGATTCTTTTCTCTCCTCCACCCAAGCGAGCTTGCTCACGAAGTGCGATGAGCTCTTTTACTTTTCAAGCTGGTTACTCATTGTATTTTGATTTGTTGTTAGAAATGAACGGATTAATTATTTGTTGCCCGGCATGCA'}
Generate random sequences for the first three reads. Use the randseq
function to generate random sequences with the same length as the original sequences.
sequenceInfo = cell(3,1); rng('default'); for i = 1:3 sequenceInfo{i} = randseq(length(br.Quality{i})); end sequenceInfo
sequenceInfo = 3x1 cell
{'TTATGACGTTATTCTACTTTGATTGTGCGAGACAATGCTACCTTACCGGTCGGAACTCGATCGGTTGAACTC' }
{'TATCACGCCTGGTCTTCGAAGTTAGCACATCGAGCGGGCAATATGTACATATTTACCTCTACAATGGATGCGCAAAAACATTCCCTCATCACAATTGAACTAAAGGGCGCGAGACGTATTCCCCG' }
{'GTTGCTGCTTGGGACCATAAAACCTCATTCACCGCGGAACCCGACTATGCGACTGGACGGCCTATTTACCGAGAGCTGTTCGAAGGCTGGTTGAATACATGGCAGAAGATTGAGGTGTCCTAAACTTACGCGGCCATAACACCTTAGCCGTCTCGGGGGAATAAGTGACCTAT'}
Update the sequences of the first three elements. br2
is a copy of br
with updated read sequences. If you need to update the br object itself, set it as the output of the function.
br2 = setSequence(br,sequenceInfo,[1:3]); br2.Sequence(1:3)
ans = 3x1 cell
{'TTATGACGTTATTCTACTTTGATTGTGCGAGACAATGCTACCTTACCGGTCGGAACTCGATCGGTTGAACTC' }
{'TATCACGCCTGGTCTTCGAAGTTAGCACATCGAGCGGGCAATATGTACATATTTACCTCTACAATGGATGCGCAAAAACATTCCCTCATCACAATTGAACTAAAGGGCGCGAGACGTATTCCCCG' }
{'GTTGCTGCTTGGGACCATAAAACCTCATTCACCGCGGAACCCGACTATGCGACTGGACGGCCTATTTACCGAGAGCTGTTCGAAGGCTGGTTGAATACATGGCAGAAGATTGAGGTGTCCTAAACTTACGCGGCCATAACACCTTAGCCGTCTCGGGGGAATAAGTGACCTAT'}
You can also update the sequences of the br object directly using dot notation.
br.Sequence(1:3) = sequenceInfo; br.Sequence(1:3)
ans = 3x1 cell
{'TTATGACGTTATTCTACTTTGATTGTGCGAGACAATGCTACCTTACCGGTCGGAACTCGATCGGTTGAACTC' }
{'TATCACGCCTGGTCTTCGAAGTTAGCACATCGAGCGGGCAATATGTACATATTTACCTCTACAATGGATGCGCAAAAACATTCCCTCATCACAATTGAACTAAAGGGCGCGAGACGTATTCCCCG' }
{'GTTGCTGCTTGGGACCATAAAACCTCATTCACCGCGGAACCCGACTATGCGACTGGACGGCCTATTTACCGAGAGCTGTTCGAAGGCTGGTTGAATACATGGCAGAAGATTGAGGTGTCCTAAACTTACGCGGCCATAACACCTTAGCCGTCTCGGGGGAATAAGTGACCTAT'}
Input Arguments
sequenceInfo
— Read sequences
cell array of character vectors | string vector
Read sequences, specified as a cell array of character vectors or string vector containing nucleotide sequences.
Example: {'TGGCTTC','AAAGCAGTACG'}
subset
— Subset of elements in object
vector of positive integers | logical vector | string vector | cell array of character vectors
Subset of elements in the object, specified as a vector of positive integers, logical vector, string vector, or cell array of character vectors containing valid sequence headers.
Example: [1 3]
Tip
When you use a sequence header (or a cell array of headers) for subset
, a
repeated header specifies all elements with that header.
Output Arguments
newObject
— New object with updated properties
BioRead
object | BioMap
object
New object with updated properties, returned as a BioRead
or BioMap
object.
Version History
Introduced in R2010a
Commande MATLAB
Vous avez cliqué sur un lien qui correspond à cette commande MATLAB :
Pour exécuter la commande, saisissez-la dans la fenêtre de commande de MATLAB. Les navigateurs web ne supportent pas les commandes MATLAB.
Select a Web Site
Choose a web site to get translated content where available and see local events and offers. Based on your location, we recommend that you select: .
You can also select a web site from the following list:
How to Get Best Site Performance
Select the China site (in Chinese or English) for best site performance. Other MathWorks country sites are not optimized for visits from your location.
Americas
- América Latina (Español)
- Canada (English)
- United States (English)
Europe
- Belgium (English)
- Denmark (English)
- Deutschland (Deutsch)
- España (Español)
- Finland (English)
- France (Français)
- Ireland (English)
- Italia (Italiano)
- Luxembourg (English)
- Netherlands (English)
- Norway (English)
- Österreich (Deutsch)
- Portugal (English)
- Sweden (English)
- Switzerland
- United Kingdom (English)