setQuality
Update quality information
Description
returns a new object that is a copy of newObject
= setQuality(object
,qualityInfo
)object
with the
Quality
property set to
qualityInfo
.
returns a new object that is a copy of newObject
= setQuality(object
,qualityInfo
,subset
)object
with the
Quality
property of a subset of elements set to
qualityInfo
. A one-to-one relationship must exist between
the number and order of elements in qualityInfo
and
subset
.
Examples
Update Quality Information
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 quality information for the first three elements of the object.
br.Quality(1:3)
ans = 3x1 cell
{'<A<<@=+><'<<<<>8<>8<<<>;&<=7>8=9#<;<?9<<<<?9<<<<A;<<A<<<@:<<<<>7<?<)<;A;' }
{'A<<<;<<<<@:<<<;;A;;A;@=*<<<<A>+<<<A;<<<<<<;;;<;<<@;@9<;<<B<B?.@9<@:A>,<?<)<<<A<<B@81*"<<<<A<A=A<<<<;<<<<<;<<:<<<?8@:8<@:<A;?8' }
{'<<<<<<;A;<<<<@=*:?9CA90(<6;9;<;<;A<<<;B<<B@5&<;<<A;:A<<B@/A;<<;:<<@:;<;<<<;?9<<<<<<;<:;<1<CA7)7<CA7+990;;9@;A<<;:69B=<1<CA6'<9CA1<@;:>77:?<)<<A;<>8;A==6A<9A?-;@:<B?.A;+;<<:<'}
Generate random quality scores for the first three reads. Assume that the quality scores are between 0 (equivalent to the ASCII code of 33) and 60 (equivalent to the ASCII code of 93).
qualities = cell(3,1); rng('default'); for i = 1:3 qualities{i} = char(floor((93 - 33) * rand(1,length(br.Quality{i}))) + 33); end qualities
qualities = 3x1 cell
{'QW(WF&1AZZ*[Z>Q):WPZH#SYINM8H+K"1#&RJ4Z#;7NP,>;GKN1IH*(>Z5D.N0?JVZA))0S0' }
{'Q/X5,0E=6RDAX2NN7C%$@OY(C=!5*P3@*E0HJM<&.W*RA\%;'Z!ORU&80Q:W+0))UCA)TF6?9%/(,/:#WY>>5W7'O8/9&(YZC$/6R!#+GLG<A2M,J,7FO%XO>;;3?' }
{'?RPG7Q@6YUBFD-3=.S,.+.;3X:,W[;'09D0EK.(24:?&0Q"XL>C/<ZA@.>FI87\#VWP&05I)L'H>OKWV5J,"M?=WEFTQC+/V">+[K?=$I#%@&RRL)H@[GQ<:R&(+8RQ$8@:HF2:!\+'7,>5ZX$M1:AY:[3KHAJH+(\+"BUI,7<[*T'}
Update the quality information of the first three elements. br2
is a copy of br
with the updated quality scores. If you need to update the br object itself, set it as the output of the function.
br2 = setQuality(br,qualities,[1:3]); br2.Quality(1:3)
ans = 3x1 cell
{'QW(WF&1AZZ*[Z>Q):WPZH#SYINM8H+K"1#&RJ4Z#;7NP,>;GKN1IH*(>Z5D.N0?JVZA))0S0' }
{'Q/X5,0E=6RDAX2NN7C%$@OY(C=!5*P3@*E0HJM<&.W*RA\%;'Z!ORU&80Q:W+0))UCA)TF6?9%/(,/:#WY>>5W7'O8/9&(YZC$/6R!#+GLG<A2M,J,7FO%XO>;;3?' }
{'?RPG7Q@6YUBFD-3=.S,.+.;3X:,W[;'09D0EK.(24:?&0Q"XL>C/<ZA@.>FI87\#VWP&05I)L'H>OKWV5J,"M?=WEFTQC+/V">+[K?=$I#%@&RRL)H@[GQ<:R&(+8RQ$8@:HF2:!\+'7,>5ZX$M1:AY:[3KHAJH+(\+"BUI,7<[*T'}
You can update the quality scores of the br object directly by using dot notation.
br.Quality(1:3) = qualities; br.Quality(1:3)
ans = 3x1 cell
{'QW(WF&1AZZ*[Z>Q):WPZH#SYINM8H+K"1#&RJ4Z#;7NP,>;GKN1IH*(>Z5D.N0?JVZA))0S0' }
{'Q/X5,0E=6RDAX2NN7C%$@OY(C=!5*P3@*E0HJM<&.W*RA\%;'Z!ORU&80Q:W+0))UCA)TF6?9%/(,/:#WY>>5W7'O8/9&(YZC$/6R!#+GLG<A2M,J,7FO%XO>;;3?' }
{'?RPG7Q@6YUBFD-3=.S,.+.;3X:,W[;'09D0EK.(24:?&0Q"XL>C/<ZA@.>FI87\#VWP&05I)L'H>OKWV5J,"M?=WEFTQC+/V">+[K?=$I#%@&RRL)H@[GQ<:R&(+8RQ$8@:HF2:!\+'7,>5ZX$M1:AY:[3KHAJH+(\+"BUI,7<[*T'}
Input Arguments
qualityInfo
— Quality information
cell array of character vectors
Quality information of reads, specified as a cell array of character vectors or string vector.
Example: {'<A<<@=+>','A<<<;<<'}
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
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