I am reading in a binary EDF file and I have to split it into multiple smaller EDF files at specific points and then adjust some of the values inside. Overall it works quite well but when I read in the file it combines 2 character arrays with each other. Obviously everything afterwords gets corrupted as well. I am at a dead end and have no idea what I'm doing wrong.
The part of the code (writing) that has to contain the problem:
byt=fread(fid,8,'*char');
fwrite(tfid,byt,'*char');
fwrite(tfid,fread(fid,44));
%new number of records
s = records;
fwrite(tfid,s,'*char');
fseek(fid,8,0);
%test
fwrite(tfid,fread(fid,8,'*char'),'*char');
When I use the reader it combines the records (fwrite(tfid,s,'*char'))
with the value of the next variable. All variables before this are displayed correctly. The relevant code of the reader:
hdr.bytes = str2double(fread(fid,8,'*char')');
reserved = fread(fid,44);%#ok
hdr.records = str2double(fread(fid,8,'*char')');
if hdr.records == -1
beep
disp('There appears to be a problem with this file; it returns an out-of-spec value of -1 for ''numberOfRecords.''')
disp('Attempting to read the file with ''edfReadUntilDone'' instead....');
[hdr, record] = edfreadUntilDone(fname, varargin);
return
end
hdr.duration = str2double(fread(fid,8,'*char')');
The likely problem is that your character array s does not have 8 characters in it, but you expect there to be 8 when you read it from the file. Whatever the number of characters in the array is, that's how many values fwrite will write out to the file. Anything less than 8 characters and you'll end up reading part of the next piece of data when you read from the file.
One fix would be to pad s with blanks before writing it:
s = [blanks(8-numel(records)) records];
In addition, the syntax '*char' is only valid when using fread: the * indicates that the output class should be 'char' as well. It's unnecessary when using fwrite.
[Edited:] I have a file data2007a.csv and I copied and pasted (using TextEdit in MacBook) the first consecutive few lines to a new file datatest1.csv for testing:
Nomenclature,ReporterISO3,ProductCode,ReporterName,PartnerISO3,PartnerName,Year,TradeFlowName,TradeFlowCode,TradeValue in 1000 USD
S3,ABW,0,Aruba,ANT,Netherlands Antilles,2007,Export,6,448.91
S3,ABW,0,Aruba,ATG,Antigua and Barbuda,2007,Export,6,0.312
S3,ABW,0,Aruba,CHN,China,2007,Export,6,24.715
S3,ABW,0,Aruba,COL,Colombia,2007,Export,6,95.885
S3,ABW,0,Aruba,DOM,Dominican Republic,2007,Export,6,11.432
I wanted to use textscan to read it into MATLAB with only columns 2,3,5 (starting from the second row) and I wrote the following code
clc,clear all
fid = fopen('datatest1.csv');
data = textscan(fid,'%*s %s %d %*s %s %*[^\n]',...
'Delimiter',',',...
'HeaderLines',1);
fclose(fid);
But I ended up with only the second row of columns 2,3 and 5:
I then keep the first row in data2007a.csv and selected several others to saved as datatest2.csv:
Nomenclature,ReporterISO3,ProductCode,ReporterName,PartnerISO3,PartnerName,Year,TradeFlowName,TradeFlowCode,TradeValue in 1000 USD
S3,ABW,1,Aruba,USA,United States,2007,Export,6,1.392
S3,ABW,1,Aruba,VEN,Venezuela,2007,Export,6,5633.157
S3,ABW,2,Aruba,ANT,Netherlands Antilles,2007,Export,6,310.734
S3,ABW,2,Aruba,USA,United States,2007,Export,6,342.42
S3,ABW,2,Aruba,VEN,Venezuela,2007,Export,6,63.722
S3,AGO,0,Angola,DEU,Germany,2007,Export,6,105.334
S3,AGO,0,Angola,ESP,Spain,2007,Export,6,8533.125
And I wrote:
clc,clear all
fid = fopen('datatest2.csv');
data = textscan(fid,'%*s %s %d %*s %s %*[^\n]',...
'Delimiter',',',...
'HeaderLines',1);
fclose(fid);
data{1}
It gives exactly what I wanted:
When I use the same code for my original data file data2007a.csv, it goes as in the first case.
What is going wrong and how can I fix it?
[Added:] If one replicates my experiments1, one can find that both cases work and the problem does not exist! I really don't know what is going on.
1 For "replicate" I mean copy-and-paste the data given above and save it as two new files, say, datatest4a.csv and datatest4b.csv. I used visdiff('datatest1.csv', 'datatest4a.csv') to compare two files and it returned:
Given how you fixed it, I think this is an end-of-line character issue. This sometimes comes up when moving text files between Windows and Unix based systems, as they use different conventions.
When you add %*[^\n] to the end of a textscan format, as you have here. it means to skip everything to the end of line. But if it expects a specific end of line character, and can't find one, it will skip everything to the end of the file. This would explain why you get one row correctly read and then nothing else.
If you don't specify what the end of line character is, Matlab appears to default to... something... in this not very clear specification in the help:
The default end-of-line sequence is \n, \r, or \r\n, depending on the contents of your file.
One way to try and cure this without having to create a new file would be to add this 'EndOfLine', '\r\n' to your textscan call:
If you specify '\r\n', then textscan treats any of \r, \n, and the
combination of the two (\r\n) as end-of-line characters.
This will hopefully handle most standard(ish) EOL conventions. It is likely that copy-pasting and saving with a different bit of software than was originally used to create the file changed the end of line characters such that Matlab was able to recognise them.
I want to read and write the same file simultaneously. Here is a simplified code:
clc;
close all;
clearvars;
fd = fopen ('abcd.txt','r+'); %opening file abcd.txt given below
while ~feof(fd)
nline = fgetl(fd);
find1 = strfind(nline,'abcd'); %searching for matching string
chk1 = isempty(find1);
if(chk1==0)
write = '0000'; %in this case, matching pattern found
% then replace that line by 0000
fprintf(fd,'%s \n',write);
else
continue;
end
end
File abcd.txt
abcde
abcd23
abcd2
abcd355
abcd65
I want to find text abcd in string of each line and replace the entire line by 0000. However, there is no change in the text file abcd.txt. The program doesn't write anything in the text file.
Someone can say read each line and write a separate text file line by line. However, there is a problem in this approach. In the original problem, instead of finding matching text `abcd, there is array of string with thousands of elements. In that case, I want to read the file, parse the file for find matching string, replace string as per condition, go to next iteration to search next matching string and so on. So in this approach, line by line reading original file and simultaneously writing another file does not work.
Another approach can be reading the entire file in memory, replacing the string and iterate. But I am not very sure how will it work. Another issue is memory usage.
Any comments?
What you are attempting to do is not possible in a efficient way. Replacing abcde with 0000, which should be done for the first line, would require all remaining text forward because you remove one char.
Instead solve this reading one file and write to a second, then remove the original file and rename the new one.
So me being the 'noob' that I am, being introduced to programming via Perl just recently, I'm still getting used to all of this. I have a .fasta file which I have to use, although I'm unsure if I'm able to open it, or if I have to work with it 'blindly', so to speak.
Anyway, the file that I have contains DNA sequences for three genes, written in this .fasta format.
Apparently it's something like this:
>label
sequence
>label
sequence
>label
sequence
My goal is to write a script to open and read the file, which I have gotten the hang of now, but I have to read each sequence, compute relative amounts of 'G' and 'C' within each sequence, and then I'm to write it to a TAB-delimited file the names of the genes, and their respective 'G' and 'C' content.
Would anyone be able to provide some guidance? I'm unsure what a TAB-delimited file is, and I'm still trying to figure out how to open a .fasta file to actually see the content. So far I've worked with .txt files which I can easily open, but not .fasta.
I apologise for sounding completely bewildered. I'd appreciate your patience. I'm not like you pros out there!!
I get that it's confusing, but you really should try to limit your question to one concrete problem, see https://stackoverflow.com/faq#questions
I have no idea what a ".fasta" file or 'G' and 'C' is.. but it probably doesn't matter.
Generally:
Open input file
Read and parse data. If it's in some strange format that you can't parse, go hunting on http://metacpan.org for a module to read it. If you're lucky someone has already done the hard part for you.
Compute whatever you're trying to compute
Print to screen (standard out) or another file.
A "TAB-delimite" file is a file with columns (think Excel) where each column is separated by the tab ("\t") character. As quick google or stackoverflow search would tell you..
Here is an approach using 'awk' utility which can be used from the command line. The following program is executed by specifying its path and using awk -f <path> <sequence file>
#NR>1 means only look at lines above 1 because you said the sequence starts on line 2
NR>1{
#this for-loop goes through all bases in the line and then performs operations below:
for (i=1;i<=length;i++)
#for each position encountered, the variable "total" is increased by 1 for total bases
total++
}
{
for (i=1;i<=length;i++)
#if the "substring" i.e. position in a line == c or g upper or lower (some bases are
#lowercase in some fasta files), it will carry out the following instructions:
if(substr($0,i,1)=="c" || substr($0,i,1)=="C")
#this increments the c count by one for every c or C encountered, the next if statement does
#the same thing for g and G:
c++; else
if(substr($0,i,1)=="g" || substr($0,i,1)=="G")
g++
}
END{
#this "END-block" prints the gene name and C, G content in percentage, separated by tabs
print "Gene name\tG content:\t"(100*g/total)"%\tC content:\t"(100*c/total)"%"
}
I have a file full of ascii data. How would I append a string to the first line of the file? I cannot find that sort of functionality using fopen (it seems to only append at the end and nothing else.)
The following is a pure MATLAB solution:
% write first line
dlmwrite('output.txt', 'string 1st line', 'delimiter', '')
% append rest of file
dlmwrite('output.txt', fileread('input.txt'), '-append', 'delimiter', '')
% overwrite on original file
movefile('output.txt', 'input.txt')
Option 1:
I would suggest calling some system commands from within MATLAB. One possibility on Windows is to write your new line of text to its own file and then use the DOS for command to concatenate the two files. Here's what the call would look like in MATLAB:
!for %f in ("file1.txt", "file2.txt") do type "%f" >> "new.txt"
I used the ! (bang) operator to invoke the command from within MATLAB. The command above sequentially pipes the contents of "file1.txt" and "file2.txt" to the file "new.txt". Keep in mind that you will probably have to end the first file with a new line character to get things to append correctly.
Another alternative to the above command would be:
!for %f in ("file2.txt") do type "%f" >> "file1.txt"
which appends the contents of "file2.txt" to "file1.txt", resulting in "file1.txt" containing the concatenated text instead of creating a new file.
If you have your file names in strings, you can create the command as a string and use the SYSTEM command instead of the ! operator. For example:
a = 'file1.txt';
b = 'file2.txt';
system(['for %f in ("' b '") do type "%f" >> "' a '"']);
Option 2:
One MATLAB only solution, in addition to Amro's, is:
dlmwrite('file.txt',['first line' 13 10 fileread('file.txt')],'delimiter','');
This uses FILEREAD to read the text file contents into a string, concatenates the new line you want to add (along with the ASCII codes for a carriage return and a line feed/new line), then overwrites the original file using DLMWRITE.
I get the feeling Option #1 might perform faster than this pure MATLAB solution for huge text files, but I don't know that for sure. ;)
How about using the frewind(fid) function to take the pointer to the beginning of the file?
I had a similar requirement and tried frewind() followed by the necessary fprintf() statement.
But, warning: It will overwrite on whichever is the 1st line. Since in my case, I was the one writing the file, I put a dummy data at the starting of the file and then at the end, let that be overwritten after the operations specified above.
BTW, even I am facing one problem with this solution, that, depending on the length(/size) of the dummy data and actual data, the program either leaves part of the dummy data on the same line, or bring my new data to the 2nd line..
Any tip in this regards is highly appreciated.