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  • Converting FASTQ to FASTA with SED/AWK

    - by neversaint
    I have a data in that always comes in block of four in the following format (called FASTQ): @SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN +SRR018006.2016 GA2:6:1:20:650 length=36 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+! @SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +SRR018006.19405469 GA2:6:100:1793:611 length=36 7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/ Is there a simple sed/awk/bash way to convert them into this format (called FASTA): >SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN >SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC In principle we want to extract the first two lines in each block-of-4 and replace @ with >.

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  • Vim syntax highlighting: make region only match on one line

    - by sixtyfootersdude
    Hello I have defined a custom file type with these lines: syn region SubSubtitle start=+=+ end=+=+ highlight SubSubtitle ctermbg=black ctermfg=DarkGrey syn region Subtitle start=+==+ end=+==+ highlight Subtitle ctermbg=black ctermfg=DarkMagenta syn region Title start=+===+ end=+===+ highlight Title ctermbg=black ctermfg=yellow syn region MasterTitle start=+====+ end=+====+ highlight MasterTitle cterm=bold term=bold ctermbg=black ctermfg=LightBlue I enclose all of my headings in this kind of document like this: ==== Biggest Heading ==== // this will be bold and light blue ===Sub heading === // this will be yellow bla bla bla // this will be normally formatted However right now when ever I use an equals sign in my code it thinks that it is a title. Is there anyway that I can force a match to be only on one line?

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  • Using pthread to perform matrix multiplication

    - by shadyabhi
    I have both matrices containing only ones and each array has 500 rows and columns. So, the resulting matrix should be a matrix of all elements having value 500. But, I am getting res_mat[0][0]=5000. Even other elements are also 5000. Why? #include<stdio.h> #include<pthread.h> #include<unistd.h> #include<stdlib.h> #define ROWS 500 #define COLUMNS 500 #define N_THREADS 10 int mat1[ROWS][COLUMNS],mat2[ROWS][COLUMNS],res_mat[ROWS][COLUMNS]; void *mult_thread(void *t) { /*This function calculates 50 ROWS of the matrix*/ int starting_row; starting_row = *((int *)t); starting_row = 50 * starting_row; int i,j,k; for (i = starting_row;i<starting_row+50;i++) for (j=0;j<COLUMNS;j++) for (k=0;k<ROWS;k++) res_mat[i][j] += (mat1[i][k] * mat2[k][j]); return; } void fill_matrix(int mat[ROWS][COLUMNS]) { int i,j; for(i=0;i<ROWS;i++) for(j=0;j<COLUMNS;j++) mat[i][j] = 1; } int main() { int n_threads = 10; //10 threads created bcos we have 500 rows and one thread calculates 50 rows int j=0; pthread_t p[n_threads]; fill_matrix(mat1); fill_matrix(mat2); for (j=0;j<10;j++) pthread_create(&p[j],NULL,mult_thread,&j); for (j=0;j<10;j++) pthread_join(p[j],NULL); printf("%d\n",res_mat[0][0]); return 0; }

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  • How to do a join of 3 files with awk by first Column?

    - by noinflection
    i have three similar files, they are all like this: ID1 Value1a ID2 Value2a . . . IDN Value2n and i want an output like this ID1 Value1a Value1b Value1c ID2 Value2a Value2b Value2c ..... IDN ValueNa ValueNb ValueNc Looking to the first line i want value1A to be the value of id1 in fileA, value1B the value of id1 in fileB, etc, i think of it like a nice sql join. I've tried several things but none of them where even close.

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  • bash and flock (file lock) - Doesn't seem to be locking....

    - by Rory
    I am playing with using flock, a bash command for file locks to prevent 2 different instances of the code from running more than once. I am using this testing code: ( ( flock -x 200 ; sleep 10 ; echo "original finished" ; ) 200>./test.lock ) & ( sleep 2 ; ( flock -x -w 2 200 ; echo "a finished" ) 200>./test.lock ) & I am running 2 subshells (backgrounded). The (flock NUM; ...) NUM>FILE syntax is from flock's man page. I expect that the first subshell will get an exclusive lock on test.lock, then wait 10 seconds, then print "original finished", all the time holding the lock. The second subshell will start at more or less the same time, wait 2 seconds, then try to get a lock on test.lock, but timeout after 2 seconds. If it gets a lock, then it'll print "a finished". If it doesn't get the lock, that subshell should stop, and nothing should be printed. Since the first subshell is waiting longer, it will keep the lock for 10 seconds, so the second subshell should not get the lock, and shouldn't finish. i.e. one should see "original finished" printed and not both. What actually happens is that "a finished" is printed, then "original finished" is printed. This implies that that the second subshell is either (a) not using the same lock as the first subhsell or (b) that it fails to get the lock, but continues to execute or (c) something else. Why don't those locks work?

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  • Replacing Part of Text Using Sed

    - by neversaint
    I have the following text file Eif2ak1.aSep07 Eif2ak1.aSep07 LOC100042862.aSep07-unspliced NADH5_C.0.aSep07-unspliced LOC100042862.aSep07-unspliced NADH5_C.0.aSep07-unspliced What I want to do is to remove all the text starting from period (.) to the end. But why this command doesn't do it? sed 's/\.*//g' myfile.txt What's the right way to do it?

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  • sed/awk or other: increment a number by 1 keeping spacing characters

    - by WizardOfOdds
    I've got a string: (notice the spacing) eh oh 37 and I want it to become: eh oh 36 (so I want to keep the spacing) Using awk I don't find how to do it, so far I have: echo "eh oh 37" | awk '$3>=0&&$3<=99 {$3--} {print}' But this gives: eh oh 36 (the spacing characters where lost, because the field separator is ' ') Is there a way to ask awk something like "print the output using the exact same field separators as the input had"? Then I tried with sed, but got stuck after this: echo "eh oh 37" | sed -e 's/\([0-9][0-9]\)/.../' Can I do arithmetic from sed using a reference to the matching digits and have the output not modify the number of spacing characters? Note that it's related to my question concerning Emacs and how to apply this to some (big) Emacs region (using a replace region with Emacs's shell-command-on-region) but it's not an identical question: this one is specifically about how to "keep spaces" when working with awk/sed/etc.

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  • Core dump of a multithreaded program

    - by benjamin button
    Hi, i have regularly worked with single threaded programs. i never saw a multithreded program crashing since i havent worked on any. is there any difference between both teh core dumps? is there any additional information provided in the core dump of a multithreaded program when compared to a single threaded program?

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  • Why can't I pipe the output of uuencode to mailx in a single Perl open statement?

    - by CheeseConQueso
    Here's my code that is not working: print "To: "; my $to=<>; chomp $to; print "From: "; my $from=<>; chomp $from; print "Attach: "; my $attach=<>; chomp $attach; print "Subject: "; my $subject=<>; chomp $subject; print "Message: "; my $message=<>; chomp $message; my $mail_fh = \*MAIL; open $mail_fh, "uuencode $attach $attach |mailx -m -s \"$subject\" -r $from $to"; print $mail_fh $message; close($mail_fh); The mailx command works fine off the command line, but not in this Perl script context. Any idea what I'm missing? I suspect that this line's format/syntax: open $mail_fh, "uuencode $attach $attach |mailx -m -s \"$subject\" -r $from $to"; is the culprit.

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  • Bash: Extract Range with Regular Expressioin (maybe sed?)

    - by sixtyfootersdude
    I have a file that is similar to this: <many lines of stuff> SUMMARY: <some lines of stuff> END OF SUMMARY I want to extract just the stuff between SUMMARY and END OF SUMMARY. I suspect I can do this with sed but I am not sure how. I know I can modify the stuff in between with this: sed "/SUMMARY/,/END OF SUMMARY/ s/replace/with/" fileName (But not sure how to just extract that stuff). I am Bash on Solaris.

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  • Pulling a timestamp from an XML feed with PHP but seem to be to many digits

    - by Craig Ward
    I am pulling a timestamp from a feed and it gives 12 digits (1269088723811). When I convert it, it comes out as 1901-12-13 20:45:52, but if I put the timestamp into http://www.epochconverter.com/ it comes out as Sat, 20 Mar 2010 12:38:43 GMT, which is the correct time. epochconverter.com mentions that it maybe in milliseconds so I have amended the script to take care of it using $mil = $timestamp; $seconds = $mil / 1000; $date = date('Y-m-d H:i:s', date($seconds)); but it still converts the date wrong, 1970-01-25 20:31:23. What am I doing wrong?

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  • Why does Samba/CIFS suck so badly. [closed]

    - by sean
    Seriously, machines refusing to save data because files THEY HAVE OPEN are locked BY THEMSELVES. Getting 200+ connections simultaneously takes it out despite a plethora of available disk and network bandwidth. You can't turn off CUPS you have to COMPILE WITHOUT IT. DFS support is completely broken and pretty much useless in the current state (as in DFS for load balancing, not replication). We should just move to NFS and find a DFS like namespace aggregator.

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  • Renaming and Moving Files in Bash or Perl

    - by Katie
    HI, I'm completely new to Bash and StackOverflow. I need to move a set of files (all contained in the same folder) to a target folder where files with the same name could already exist. In case a specific file exists, I need to rename the file before moving it, by appending for example an incremental integer to the file name. The extensions should be preserved (in other words, that appended incremental integer should go before the extension). The file names could contain dots in the middle. Originally, I was thinking about comparing the two folders to have a list of the existing files (I did this with "comm"), but then I got a bit stuck. I think I'm just trying to do things in the most complicated possible way. Any hint to do this in the "bash way"? It's OK if it is done in a script other than bash script.

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  • naming a screen session in linux

    - by Aly
    Hi, I am running multiple screens from one ssh connection, when I list all of the screens via screen -ls the names are not very descriptive and when I have multiple screens it becomes hard to remember what is running on each. Does anyone know how to name these sessions (preferably when creating the screen). Thanks

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  • Keyboard input: how to separate keycodes received from user

    - by Iulian Serbanoiu
    Hello, I am writing an application involving user input from the keyboard. For doing it I use this way of reading the input: #include <stdio.h> #include <termios.h> #include <unistd.h> int mygetch( ) { struct termios oldt, newt; int ch; tcgetattr( STDIN_FILENO, &oldt ); newt = oldt; newt.c_lflag &= ~( ICANON | ECHO ); tcsetattr( STDIN_FILENO, TCSANOW, &newt ); ch = getchar(); tcsetattr( STDIN_FILENO, TCSANOW, &oldt ); return ch; } int main(void) { int c; do{ c = mygetch(); printf("%d\n",c); }while(c!='q'); return 0; } Everyting works fine for letters digits,tabs but when hiting DEL, LEFT, CTRL+LEFT, F8 (and others) I receive not one but 3,4,5 or even 6 characters. The question is: Is is possible to make a separation of these characters (to actually know that I only hit one key or key combination). What I would like is to have a function to return a single integer value for any type of input (letter, digit, F1-F12, DEl, PGUP, PGDOWN, CTRL+A, CTRL+ALT+A, ALT+LEFT, etc). Is this possible? I'm interested in an idea to to this, the language doesn't matter much, though I'd prefer perl or c. Thanks, Iulian

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  • Crazy interview question

    - by benjamin button
    I was asked this crazy question. I was out of my wits. Can a method in base class which is declared as virtual be called using the base class pointer which is pointing to a derived class object? Is this possible?

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  • Write STDOUT & STDERR to a logfile, also write STDERR to screen

    - by Stefan Lasiewski
    I would like to run several commands, and capture all output to a logfile. I also want to print any errors to the screen (or optionally mail the output to someone). Here's an example. The following command will run three commands, and will write all output (STDOUT and STDERR) into a single logfile. { command1 && command2 && command3 ; } > logfile.log 2>&1 Here is what I want to do with the output of these commands: STDERR and STDOUT for all commands goes to a logfile, in case I need it later--- I usually won't look in here unless there are problems. Print STDERR to the screen (or optionally, pipe to /bin/mail), so that any error stands out and doesn't get ignored. It would be nice if the return codes were still usable, so that I could do some error handling. Maybe I want to send email if there was an error, like this: { command1 && command2 && command3 ; } logfile.log 2&1 || mailx -s "There was an error" [email protected] The problem I run into is that STDERR loses context during I/O redirection. A '2&1' will convert STDERR into STDOUT, and therefore I cannot view errors if I do 2 error.log Here are a couple juicier examples. Let's pretend that I am running some familiar build commands, but I don't want the entire build to stop just because of one error so I use the '--keep-going' flag. { ./configure && make --keep-going && make install ; } > build.log 2>&1 Or, here's a simple (And perhaps sloppy) build and deploy script, which will keep going in the event of an error. { ./configure && make --keep-going && make install && rsync -av --keep-going /foo devhost:/foo} > build-and-deploy.log 2>&1 I think what I want involves some sort of Bash I/O Redirection, but I can't figure this out.

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  • How do I determine if a terminal is color-capable?

    - by asjo
    I would like to change a program to automatically detect whether a terminal is color-capable or not, so when I run said program from within a non-color capable terminal (say M-x shell in (X)Emacs), color is automatically turned off. I don't want to hardcode the program to detect TERM={emacs,dumb}. I am thinking that termcap/terminfo should be able to help with this, but so far I've only managed to cobble together this (n)curses-using snippet of code, which fails badly when it can't find the terminal: #include <stdlib.h> #include <curses.h> int main(void) { int colors=0; initscr(); start_color(); colors=has_colors() ? 1 : 0; endwin(); printf(colors ? "YES\n" : "NO\n"); exit(0); } I.e. I get this: $ gcc -Wall -lncurses -o hep hep.c $ echo $TERM xterm $ ./hep YES $ export TERM=dumb $ ./hep NO $ export TERM=emacs $ ./hep Error opening terminal: emacs. $ which is... suboptimal.

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  • How to include clean target in makefile

    - by neversaint
    I have a makefile that looks like this CXX = g++ -O2 -Wall all: code1 code2 code1: code1.cc utilities.cc $(CXX) $^ -o $@ code2: code2.cc utilities.cc $(CXX) $^ -o $@ What I want to do next is to include 'clean target' so that every time I run 'make' it will automatically delete the existing binary files of code1 and code2 before creating the new ones. I tried to put these lines at the very end of the makefile, but it doesn't work clean: rm -f $@ echo Clean done What's the right way to do it?

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