I searched the documentation about the fastaread function, but I'm still kind of confused about the Sequence part.
So, suppose my file is stored in the file_path location, and fastaread(file_path) will return the data obtained.
fastaread returns two columns, one is with title header and the other one is with title sequence. Then, fastaread(file_path).sequence will return the sequence column? Does that mean that fastaread(file_path).sequence is a column vector?
Actually it's a row vector containing characters.
Example with data provided with Matlab:
p53nt = fastaread('p53nt.txt')
gives a structure with 2 fields: Header and Sequence.
p53nt.Header gives info about the actual sequence:
p53nt.Header
ans =
gi|8400737|ref|NM_000546.2| Homo sapiens tumor protein p53 (Li-Fraumeni syndrome) (TP53), mRNA
while p53nt.Sequence gives a character array of size 1xN:
S = p53nt.Sequence
S =
ACTTGTCATGGCGACTGTCCAGC... And so on
Typing whos S gives this:
Name Size Bytes Class Attributes
S 1x2629 5258 char
So if you want a column vector for some reason, use the colon operator:
S = S(:);
Hope its a bit clearer now!
Related
I created a list of names of data files, e.g. abc123.xml, abc456.xml, via
list = dir('folder/*.xml').
Matlab starts this out as a 10x1 struct with 5 fields, where the first one is the name. I extracted the needed data with struct2table, so I now got a 10x1 table. I only need the numerical value as 10x1 double. How can I get rid of the alphanumerical stuff and change the data type?
I tried regexp (Undefined function 'regexp' for input arguments of type 'table') and strfind (Conversion to double from table is not possible). Couldn't come up with anything else, as I'm very new to Matlab.
You can extract the name fields and place them in a cell array, use regexp to capture the first string of digits it finds in each name, then use str2double to convert those to numeric values:
strs = regexp({list.name}, '(\d+)', 'once', 'tokens');
nums = str2double([strs{:}]);
What is the difference between string and character class in MATLAB?
a = 'AX'; % This is a character.
b = string(a) % This is a string.
The documentation suggests:
There are two ways to represent text in MATLAB®. You can store text in character arrays. A typical use is to store short pieces of text as character vectors. And starting in Release 2016b, you can also store multiple pieces of text in string arrays. String arrays provide a set of functions for working with text as data.
This is how the two representations differ:
Element access. To represent char vectors of different length, one had to use cell arrays, e.g. ch = {'a', 'ab', 'abc'}. With strings, they can be created in actual arrays: str = [string('a'), string('ab'), string('abc')].
However, to index characters in a string array directly, the curly bracket notation has to be used:
str{3}(2) % == 'b'
Memory use. Chars use exactly two bytes per character. strings have overhead:
a = 'abc'
b = string('abc')
whos a b
returns
Name Size Bytes Class Attributes
a 1x3 6 char
b 1x1 132 string
The best place to start for understanding the difference is the documentation. The key difference, as stated there:
A character array is a sequence of characters, just as a numeric array is a sequence of numbers. A typical use is to store short pieces of text as character vectors, such as c = 'Hello World';.
A string array is a container for pieces of text. String arrays provide a set of functions for working with text as data. To convert text to string arrays, use the string function.
Here are a few more key points about their differences:
They are different classes (i.e. types): char versus string. As such they will have different sets of methods defined for each. Think about what sort of operations you want to do on your text, then choose the one that best supports those.
Since a string is a container class, be mindful of how its size differs from an equivalent character array representation. Using your example:
>> a = 'AX'; % This is a character.
>> b = string(a) % This is a string.
>> whos
Name Size Bytes Class Attributes
a 1x2 4 char
b 1x1 134 string
Notice that the string container lists its size as 1x1 (and takes up more bytes in memory) while the character array is, as its name implies, a 1x2 array of characters.
They can't always be used interchangeably, and you may need to convert between the two for certain operations. For example, string objects can't be used as dynamic field names for structure indexing:
>> s = struct('a', 1);
>> name = string('a');
>> s.(name)
Argument to dynamic structure reference must evaluate to a valid field name.
>> s.(char(name))
ans =
1
Strings do have a bit of overhead, but still increase by 2 bytes per character. After every 8 characters it increases the size of the variable. The red line is y=2x+127.
figure is created using:
v=[];N=100;
for ct = 1:N
s=char(randi([0 255],[1,ct]));
s=string(s);
a=whos('s');v(ct)=a.bytes;
end
figure(1);clf
plot(v)
xlabel('# characters')
ylabel('# bytes')
p=polyfit(1:N,v,1);
hold on
plot([0,N],[127,2*N+127],'r')
hold off
One important practical thing to note is, that strings and chars behave differently when interacting with square brackets. This can be especially confusing when coming from python. consider following example:
>>['asdf' '123']
ans =
'asdf123'
>> ["asdf" "123"]
ans =
1×2 string array
"asdf" "123"
I want to use fscanf for reading a text file containing 4 rows with an unknown number of columns. The newline is represented by two consecutive spaces.
It was suggested that I pass : as the sizeA parameter but it doesn't work.
How can I read in my data?
update: The file format is
String1 String2 String3
10 20 30
a b c
1 2 3
I have to fill 4 arrays, one for each row.
See if this will work for your application.
fid1=fopen('test.txt');
i=1;
check=0;
while check~=1
str=fscanf(fid1,'%s',1);
if strcmp(str,'')~=1;
string(i)={str};
end
i=i+1;
check=strcmp(str,'');
end
fclose(fid1);
X=reshape(string,[],4);
ar1=X(:,1)
ar2=X(:,2)
ar3=X(:,3)
ar4=X(:,4)
Once you have 'ar1','ar2','ar3','ar4' you can parse them however you want.
I have found a solution, i don't know if it is the only one but it works fine:
A=fscanf(fid,'%[^\n] *\n')
B=sscanf(A,'%c ')
Z=fscanf(fid,'%[^\n] *\n')
C=sscanf(Z,'%d')
....
You could use
rawText = getl(fid);
lines = regexp(thisLine,' ','split);
tokens = {};
for ix = 1:numel(lines)
tokens{end+1} = regexp(lines{ix},' ','split'};
end
This will give you a cell array of strings having the row and column shape or your original data.
To read an arbitrary line of text then break it up according the the formating information you have available. My example uses a single space character.
This uses regular expressions to define the separator. Regular expressions powerful but too complex to describe here. See the MATLAB help for regexp and regular expressions.
I have the following sample from a CSV file. Structure is:
Date ,Time(Hr:Min:S:mS), Value
2015:08:20,08:20:19:123 , 0.05234
2015:08:20,08:20:19:456 , 0.06234
I then would like to read this into a matrix in MATLAB.
Attempt :
Matrix = csvread('file_name.csv');
Also tried an attempt formatting the string.
fmt = %u:%u:%u %u:%u:%u:%u %f
Matrix = csvread('file_name.csv',fmt);
The problem is when the file is read the format is wrong and displays it differently.
Any help or advice given would be greatly appreciated!
EDIT
When using #Adriaan answer the result is
2015 -11 -9
8 -17 -1
So it seems that MATLAB thinks the '-' is the delimiter(separator)
Matrix = csvread('file_name.csv',1,0);
csread does not support a format specifier. Just enter the number of header rows (I took it to be one, as per example), and number of header columns, 0.
You file, however, contains non-numeric data. Thus import it with importdata:
data = importdata('file_name.csv')
This will get you a structure, data with two fields: data.data contains the numeric data, i.e. a vector containing your value. data.textdata is a cell containing the rest of the data, you need the first two column and extract the numerics from it, i.e.
for ii = 2:size(data.textdata,1)
tmp1 = data.textdata{ii,1};
Date(ii,1) = datenum(tmp1,'YYYY:MM:DD');
tmp2 = data.textdata{ii,2};
Date(ii,2) = datenum(tmp2,'HH:MM:SS:FFF');
end
Thanks to #Excaza it turns out milliseconds are supported.
I think I'm losing my mind.
I have a 3 x 2 cell which looks exactly like below.
Region Code
US 1
EU 2
I then have the following code to determine the row number for the EU region.
eq_code_index = find(ismember(fund.type_des(:, 1), 'EU'));
eq_code = cell2mat(fund.type_des(eq_code_index, 2));
eq_code_index returns 3 which is correct (row headers are included in the output). So I want the value in row 3, column 2 which is 2. I then use cell2mat to convert it from a cell value to an integer however it doesn't work the value is of type char? Haven't a clue why cell2mat isn't working?
Update
Even if I do the following two lines of code below I can't get the codes into a vector, they turn into char's
codes = fund.type_des(2:end, end);
codes = cell2mat(codes)
To access a single element in a cell array, use curly braces:
fund.type_des{eq_code_index, 2};
This is generally simpler than using cell2mat(). If the contents of the cell are chars and you want an integer, you have to perform the conversion. str2num() is one of many options for this:
eq_code = str2num(fund.type_des{eq_code_index, 2});