I would like to take an input from the user and make this input a file name which I will be writing on my code after taking the input.
I would be appreciated if you could help me on this.
Thanks in advance!
MATLAB
filename = input('File name: ','s');
fileID = fopen(filename)
fprintf(fileID, 'That wasn''t so hard')
fclose(fileID)
input - Request user input
fopen - Open file, or obtain information about open files
fprintf - Write data to text file
Python
filename = raw_input('File name: ')
with open(filename, 'w') as f:
f.write('That wasn\'t so hard')
C
#include <stdio.h>
int main() {
char filename[81];
FILE* f;
while (1) {
printf("File name: ");
if (scanf("%80s") == 1) break;
}
f = fopen(filename, "w");
if (!f) {
perror("opening file");
return 1;
}
fprintf(f, "That wasn't so hard\n");
fclose(f);
return 0;
}
sh script
#!/bin/sh
echo -n "File name: "
read filename
echo "That wasn't so hard" > $filename
Related
I'm using a large array of floats. After a lot of fiddling I've managed to write it to a binary file. When opening that file at a later time, the reading process only reads a couple of handfuls of floats (according to the return-value of fread(), and it's all values 0.0f). The reading is supposed to put the floats into an (the original) array, and it does not contain the original values.
I'm using Code::Blocks and MinGW doing a program in the 32bit realm on a 64bit pc .. and I'm not very proficient on c/c++ and pointers.
#include<...>
const int mSIZE = 6000 ;
static float data[mSIZE*mSIZE] ;
void myUseFunc(){
const char *chN = "J:/path/flt_632_55.bin" ;
FILE *outFile=NULL ;
# .. sucessfully filling and using data[]
..
size_t st = mSIZE*mSIZE ;
outFile = fopen( chN , "w" ) ;
if(!outFile){ printf("error opening file %s \n", chN); exit(0);}
else{
size_t indt;
indt = fwrite( data , sizeof(float), st , outFile );
std::cout << "floats written to file: " << indt << std::endl ;
#.. value shows that all values ar written
# and a properly sized file has appeared at the proper place
}
fclose( outFile ) ;
}
void myLoadFunc( const char *fileName){
FILE *inFile = NULL ;
inFile = fopen( fileName, "r");
if(!inFile){ printf("error opening file %s \n", fileName); exit(0); }
size_t blok = mSIZE*mSIZE ;
size_t out;
out = fread( dataOne, sizeof(GLfloat), blok , inFile);
fclose(inFile);
if(out != blok){
std::cout<< out << std::endl ;
fputs ("Reading error",stderr);
# no stderr presented at the console ..
printf("some error\n") ;
exit(0);
# .. program exits at out=14
}
...
}
int main( ){
...
const char *FileName = "J:/path/flt_632_55.bin" ;
myLoadFunc( FileName ) ;
...
}
You are not writing to/reading from a binary file, you open the files as text files.
You need to add the "b" to the open mode, like
outFile = fopen( chN , "wb" ) ;
I have a data file I am trying to import into redshift (postgress mpp database). I am trying to import into postgres with a '|' delimiter. But some data, has the '|' in the string data itself, for example :
73779087|"UCGr4c0_zShyHbctxJJrJ03w"|"ItsMattSpeaking | SuPra"
So I tried this sed command :
sed -i -E "s/(.+|)(.+|)|/\1\2\\|/g" inputfile.txt >outputfile.txt
Any ideas on what is wrong with the sed command, to replace the | in the last string with a \| escape character so that Redshift will not view this as a delimiter ? Any help is appreciated.
This might work for you (GNU sed):
sed -r ':a;s/^([^"]*("[^"|]*"[^"]*)*"[^"|]*)\|/\1/g;ta' file
This removes | within double quotes however it does not cater for quoted quotes, so beware!
There are somethings you don't use SED for, I'd say this is one of those things. Try using a python script with the re library or just plain string manipulation.
I think this C++ code does what you need.
// $ g++ -Wall -Wextra -std=c++11 main.cpp
#include <iostream>
int main(int, char*[]) {
bool str = false;
char c;
std::ios_base::sync_with_stdio(false);
std::cin.tie(nullptr);
while (std::cin.get(c)) {
if (c == '|') {
if (str) {
std::cout << '\\'; } }
else if (c == '"') {
// Toggle string parsing.
str = !str; }
else if (c == '\\') {
// Skip escaped chars.
std::cout << c;
std::cin.get(c); }
std::cout << c; }
return 0; }
The problem with sed in this example is you need to know more than the basics in order to track which state you are in (string or not).
Here's a script for translating a file with pipe-separated values, as described, to one following the simpler conventions of a TSV file. It assumes the availability of a PHP interpreter. If the script is saved as psv2tsv and made executable in a Mac or Linux environment, then psv2tsv -h should offer more details.
Example usage (using <TAB> to indicate a TAB in the output):
$ psv2tsv <<< $'73779087|"UCGr4c0_zShyHbctxJJrJ03w"|"ItsMattSpeaking | SuPra"'
73779087<TAB>UCGr4c0_zShyHbctxJJrJ03w<TAB>ItsMattSpeaking | SuPra<TAB>
$ psv2tsv <<< $'a|"b|c\t\d"|"e\n"'
a<TAB>b|c\t\d<TAB>e\n<TAB>
The script:
#!/usr/bin/env php
<?php
# Author: pkoppstein at gmail.com 12/2015
# Use at your own risk.
# Input - pipe-separated values along the lines of CSV.
# Translate embedded newline and tab characters.
function help() {
global $argv;
echo <<<EOT
Syntax: {$argv[0]} [filepath]
Convert a file or stream of records with pipe-separated values to the
TSV (tab-separated value) format. If no argument is specified, or if
filepath is specified as -, then input is taken from stdin.
The input is assumed to be like a CSV file but with pipe characters
(|) used instead of commas. The output follows the simpler
conventions of TSV files.
Note that each tab in the input is translated to "\\t", and each
embedded newline is translated to "\\n". Each translated record is
then written to stdout. See PHP's fgetcsv for further details.
EOT;
}
$file = ($argc > 1 ) ? $argv[1] : 'php://stdin';
if ( $file == "-h" or $file == "--help" ) {
help();
exit;
}
if ( $file == "-" ) $file = 'php://stdin';
$handle = #fopen($file, "r");
if ($handle) {
while (($data = fgetcsv($handle,0,"|")) !== FALSE) {
$num = count($data);
for ($c=0; $c < $num; $c++) {
# str_replace( mixed $search , mixed $replace , mixed $subject [, int &$count ] )
echo str_replace("\t", "\\t", str_replace("\n", "\\n", $data[$c])) . "\t";
}
echo "\n";
}
fclose($handle);
}
else {
echo "{$argv[0]}: unable to fopen $argv[1]\n";
exit(1);
}
?>
I have a text file which is an output from the command line of a diff program.
I now read the file using
fileID = fopen('runInfo.out','r');
file_dump = textscan(fileID, '%s', 'Delimiter', '\n');
% Find postion of Min Cp to mark field on interest
Row = find(~cellfun('isempty',strfind(file_dump{1}, 'Minimum Viscous Cp')));
fclose(fileID);
I now have the row from which I need to extract data.
The format of the file from this location looks something like
.OPERv c>
u/Uinf = 1.0050 v/Uinf = -0.0029
q/Uinf = 1.0050 Cp = -0.0100
.OPERv c>
u/Uinf = 1.0088 v/Uinf = -0.0075
q/Uinf = 1.0088 Cp = -0.0177
.OPERv c>
u/Uinf = 1.0156 v/Uinf = -0.0281
q/Uinf = 1.0160 Cp = -0.0323
Since I already have this data in my cellArray from textscan,
What I could think of was (pretty non robust)
u_line = vertcat(file_dump{1,1}...
{find(~cellfun('isempty',strfind(file_dump{1}, 'u/Uinf'))),1})
v = str2num(u_line(:,end-5:end));
and then somehow extract the numbers from these returned cells?
In the end, I need the four values of u/Uinf, v/Uinf, q/Uinf and Cp.
Is there a simpler option that I am missing?
If the text file from which to extract the data is the one you posted in the sedond box, you can use a AWK script.
The followng AWK script reads the text file and generates as output a MatLab .m file containing the values extracted form the text file as arrays.
AWK script
BEGIN {
u_cnt=1;
v_cnt=1;
c_cnt=1;
q_cnt=1;
}
{
if($1 == "u/Uinf")
{
u_Uinf[u_cnt]=$3
u_cnt++
}
if($4 == "v/Uinf")
{
v_Uinf[v_cnt]=$6
v_cnt++
}
if($4 == "Cp")
{
cp[c_cnt]=$6
c_cnt++
}
if($1 == "q/Uinf")
{
q_Uinf[q_cnt]=$3
q_cnt++
}
}
END {
print "u_Uinf_data=[" > "txt_file_data.m"
for(i=1;i<u_cnt;i++)
print u_Uinf[i] > "txt_file_data.m"
print "];" > "txt_file_data.m"
print "v_Uinf_data=[" > "txt_file_data.m"
for(i=1;i<v_cnt;i++)
print v_Uinf[i] > "txt_file_data.m"
print "];" > "txt_file_data.m"
print "q_Uinf_data=[" > "txt_file_data.m"
for(i=1;i<q_cnt;i++)
print q_Uinf[i] > "txt_file_data.m"
print "];" > "txt_file_data.m"
print "cp_data=[" > "txt_file_data.m"
for(i=1;i<c_cnt;i++)
print cp[i] > "txt_file_data.m"
print "];" > "txt_file_data.m"
}
Output .m file
u_Uinf_data=[
1.0050
1.0088
1.0156
];
v_Uinf_data=[
-0.0029
-0.0075
-0.0281
];
q_Uinf_data=[
1.0050
1.0088
1.0160
];
cp_data=[
-0.0100
-0.0177
-0.0323
];
I have multiple text files named split01.txt, split02.txt etc... with the data in the format below: (This is what I have)
/tmp/audio_files/n000001.wav;
/tmp/audio_files/n000002.wav;
/tmp/audio_files/n000003.wav;
/tmp/audio_files/p000004.wav;
/tmp/audio_files/p000005.wav;
I would like to create another file with the data taken from the split01.txt, split02.txt etc... file in the format below: (this is the format I would like to see)
[playlist]
NumberOfEntries=5
File000001=n000001.wav
Title000001=n000001.wav
File000002=n000002.wav
Title000002=n000002.wav
File000003=n000003.wav
Title000003=n000003.wav
File000004=p000004.wav
Title000004=p000004.wav
File000005=p000005.wav
Title000005=p000005.wav
Version=2
Can this be done in one instance? The reason I ask is that I'm going to be running/calling the command (awk,grep,sed,etc...) from inside of octave/matlab after the initial process has completed creating the audio files.
example: of what I mean in one instance below: (matlab/octave code)
system(strcat({'split --lines=3600 -d '},dirpathwaveformstmp,fileallplaylistStr,{' '},dirpathwaveformstmp,'allsplit'))
This splits a single file into multiple files with the names allsplit01 allsplit02 etc.. and each file only has a max of 3600 lines.
For those who asked this is creating playlist files for audio files I create with octave/matlab.
Any suggestions?
Here's one way you could do it with awk:
parse.awk
BEGIN {
print "[playlist]"
print "NumberOfEntries=" len "\n"
i = 1
}
{
gsub(".*/|;", "")
printf "File%06d=%s\n" , i, $0
printf "Title%06d=%s\n\n", i, $0
i++
}
END {
print "Version 2"
}
Run it like this:
awk -v len=$(wc -l < infile) -f parse.awk infile
Output:
[playlist]
NumberOfEntries=5
File000001=n000001.wav
Title000001=n000001.wav
File000002=n000002.wav
Title000002=n000002.wav
File000003=n000003.wav
Title000003=n000003.wav
File000004=p000004.wav
Title000004=p000004.wav
File000005=p000005.wav
Title000005=p000005.wav
Version 2
If you're writing your program in Octave, why don't you do it in Octave as well? The language is not limited to numerical analysis. What you're trying to do can be done quite easily with Octave functions.
filepath = "path for input file"
playlistpath = "path for output file"
## read file and prepare cell array for printing
files = strsplit (fileread (filepath)', "\n");
if (isempty (files{end}))
files(end) = [];
endif
[~, names, exts] = cellfun (#fileparts, files, "UniformOutput", false);
files = strcat (names, exts);
files(2,:) = files(1,:);
files(4,:) = files(1,:);
files(1,:) = num2cell (1:columns(files))(:);
files(3,:) = num2cell (1:columns(files))(:);
## write playlist
[fid, msg] = fopen (playlistpath, "w");
if (fid < 0)
error ("Unable to fopen %s for writing: %s", playlistpath, msg);
endif
fprintf (fid, "[playlist]\n");
fprintf (fid, "NumberOfEntries=%i\n", columns (files));
fprintf (fid, "\n");
fprintf (fid, "File%06d=%s\nTitle%06d=%s\n\n", files{:});
fprintf (fid, "Version 2");
if (fclose (fid))
error ("Unable to fclose file %s with FID %i", playlistpath, fid);
endif
I have two files:
(one.txt) looks Like this:
>ENST001
(((....)))
(((...)))
>ENST002
(((((((.......))))))
((((...)))
I have like 10000 more ENST
(two.txt) looks like this:
>ENST001 110
>ENST002 59
and so on for the rest of all ENSTs
I basically would like to replace the ENSTs in the (one.txt) by the combination of the two fields in the (two.txt) so the results will look like this:
>ENST001_110
(((....)))
(((...)))
>ENST002_59
(((((((.......))))))
((((...)))
I wrote a matlab script to do so but since it loops for all lines in (two.txt) it take like 6 hours to finish, so I think using awk, sed, grep, or even perl we can get the result in few minutes. This is what I did in matlab:
frf = fopen('one.txt', 'r');
frp = fopen('two.txt', 'r');
fw = fopen('result.txt', 'w');
while feof(frf) == 0
line = fgetl(frf);
first_char = line(1);
if strcmp(first_char, '>') == 1 % if the line in one.txt start by > it is the ID
id_fold = strrep(line, '>', ''); % Reomve the > symbol
frewind(frp) % Rewind two.txt file after each loop
while feof(frp) == 0
raw = fgetl(frp);
scan = textscan(raw, '%s%s');
id_pos = scan{1}{1};
pos = scan{2}{1};
if strcmp(id_fold, id_pos) == 1 % if both ids are the same
id_new = ['>', id_fold, '_', pos];
fprintf(fw, '%s\n', id_new);
end
end
else
fprintf(fw, '%s\n', line); % if the line doesn't start by > print it to results
end
end
One way using awk. FNR == NR process first file in arguments and saves each number. Second condition process second file, and when first field matches with a key in the array modifies that line appending the number.
awk '
FNR == NR {
data[ $1 ] = $2;
next
}
FNR < NR && data[ $1 ] {
$0 = $1 "_" data[ $1 ]
}
{ print }
' two.txt one.txt
Output:
>ENST001_110
(((....)))
(((...)))
>ENST002_59
(((((((.......))))))
((((...)))
With sed you can at first run only on two.txt you can make a sed commands to replace as you want and run it at one.txt:
First way
sed "$(sed -n '/>ENST/{s=.*\(ENST[0-9]\+\)\s\+\([0-9]\+\).*=s/\1/\1_\2/;=;p}' two.txt)" one.txt
Second way
If files are huge you'll get too many arguments error with previous way. Therefore there is another way to fix this error. You need execute all three commands one by one:
sed -n '1i#!/bin/sed -f
/>ENST/{s=.*\(ENST[0-9]\+\)\s\+\([0-9]\+\).*=s/\1/\1_\2/;=;p}' two.txt > script.sed
chmod +x script.sed
./script.sed one.txt
The first command will form the sed script that will be able to modify one.txt as you want. chmod will make this new script executable. And the last command will execute command. So each file is read only once. There is no any loops.
Note that first command consist from two lines, but still is one command. If you'll delete newline character it will break the script. It is because of i command in sed. You can look for details in ``sed man page.
This Perl solution sends the modified one.txt file to STDOUT.
use strict;
use warnings;
open my $f2, '<', 'two.txt' or die $!;
my %ids;
while (<$f2>) {
$ids{$1} = "$1_$2" if /^>(\S+)\s+(\d+)/;
}
open my $f1, '<', 'one.txt' or die $!;
while (<$f1>) {
s/^>(\S+)\s*$/>$ids{$1}/;
print;
}
Turn the problem on its head. In perl I would do something like this:
#!/usr/bin/perl
open(FH1, "one.txt");
open(FH2, "two.txt");
open(RESULT, ">result.txt");
my %data;
while (my $line = <FH2>)
{
chomp(line);
# Delete leading angle bracket
$line =~ s/>//d;
# split enst and pos
my ($enst, $post) = split(/\s+/, line);
# Store POS with ENST as key
$data{$enst} = $pos;
}
close(FH2);
while (my $line = <FH1>)
{
# Check line for ENST
if ($line =~ m/^>(ENST\d+)/)
{
my $enst = $1;
# Get pos for ENST
my $pos = $data{$enst};
# make new line
$line = '>' . $enst . '_' . $pos . '\n';
}
print RESULT $line;
}
close(FH1);
close(RESULT);
This might work for you (GNU sed):
sed -n '/^$/!s|^\(\S*\)\s*\(\S*\).*|s/^\1.*/\1_\2/|p' two.txt | sed -f - one.txt
Try this MATLAB solution (no loops):
%# read files as cell array of lines
fid = fopen('one.txt','rt');
C = textscan(fid, '%s', 'Delimiter','\n');
C1 = C{1};
fclose(fid);
fid = fopen('two.txt','rt');
C = textscan(fid, '%s', 'Delimiter','\n');
C2 = C{1};
fclose(fid);
%# use regexp to extract ENST numbers from both files
num = regexp(C1, '>ENST(\d+)', 'tokens', 'once');
idx1 = find(~cellfun(#isempty, num)); %# location of >ENST line
val1 = str2double([num{:}]); %# ENST numbers
num = regexp(C2, '>ENST(\d+)', 'tokens', 'once');
idx2 = find(~cellfun(#isempty, num));
val2 = str2double([num{:}]);
%# construct new header lines from file2
C2(idx2) = regexprep(C2(idx2), ' +','_');
%# replace headers lines in file1 with the new headers
[tf,loc] = ismember(val2,val1);
C1( idx1(loc(tf)) ) = C2( idx2(tf) );
%# write result
fid = fopen('three.txt','wt');
fprintf(fid, '%s\n',C1{:});
fclose(fid);