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  • Parsing Chunk of Data into Hash of Array With Perl

    - by neversaint
    I have data that looks like this: #info #info2 1:SRX004541 Submitter: UT-MGS, UT-MGS Study: Glossina morsitans transcript sequencing project(SRP000741) Sample: Glossina morsitans(SRS002835) Instrument: Illumina Genome Analyzer Total: 1 run, 8.3M spots, 299.9M bases Run #1: SRR016086, 8330172 spots, 299886192 bases 2:SRX004540 Submitter: UT-MGS Study: Anopheles stephensi transcript sequencing project(SRP000747) Sample: Anopheles stephensi(SRS002864) Instrument: Solexa 1G Genome Analyzer Total: 1 run, 8.4M spots, 401M bases Run #1: SRR017875, 8354743 spots, 401027664 bases 3:SRX002521 Submitter: UT-MGS Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403) Sample: Human DLD-1 tissue culture cell line(SRS001843) Instrument: Solexa 1G Genome Analyzer Total: 6 runs, 27.1M spots, 977M bases Run #1: SRR013356, 4801519 spots, 172854684 bases Run #2: SRR013357, 3603355 spots, 129720780 bases Run #3: SRR013358, 3459692 spots, 124548912 bases Run #4: SRR013360, 5219342 spots, 187896312 bases Run #5: SRR013361, 5140152 spots, 185045472 bases Run #6: SRR013370, 4916054 spots, 176977944 bases What I want to do is to create a hash of array with first line of each chunk as keys and SR## part of lines with "^Run" as its array member: $VAR = { 'SRX004541' => ['SRR016086'], # etc } But why my construct doesn't work. And it must be a better way to do it. use Data::Dumper; my %bighash; my $head = ""; my @temp = (); while ( <> ) { chomp; next if (/^\#/); if ( /^\d{1,2}:(\w+)/ ) { print "$1\n"; $head = $1; } elsif (/^Run \#\d+: (\w+),.*/){ print "\t$1\n"; push @temp, $1; } elsif (/^$/) { push @{$bighash{$head}}, [@temp]; @temp =(); } } print Dumper \%bighash ;

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  • Sorting tab delimited text file based on multiple columns in natural way [duplicate]

    - by Vignesh
    This question already has an answer here: Sorting a column of CSV file resulting in 1123 appearing before 232 1 answer I am trying to sort a file based on all two columns Eg: chr19 1070019 1070020 chr16 869712 869713 chr1 1378131 1378132 chr12 189386 189387 chr4 254941 254942 chr16 1476500 1476501 chr2 1476810 1476811 chr19 313283 313284 chr17 595817 595818 chr18 656897 656898 chr19 1061829 1061830 I Tried sort -t $\t -k1,1 2,2 <filename> but doesn't work. I want the output to be sorted by first column and second column based on first column. I want to do a natural sort. Not lexical sorting. Eg: chr1 1378131 1378132 chr2 1476810 1476811 chr4 254941 254942 chr12 189386 189387 chr16 869712 869713 chr16 1476500 1476501 chr17 595817 595818 chr18 656897 656898 chr19 313283 313284 chr19 1061829 1061830 chr19 1070019 1070020 Anyone any idea?

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  • Grep expression with special file names

    - by user2919185
    i am a real beginner in csh/tcsh scripting and that's why i need your help. The problem is I have to go through some regular files in directories and find those files, that have their own name in its content. In the following piece of script is cycle in which I am going through paths and using grep to find the file's name in its content. What is surely correct is $something:q - is array of paths where i have to find files. The next variable is name in which is only name of current file. for example: /home/computer/text.txt (paths) and: text.txt (name) And my biggest problem is to find names of files in their content. It's quite difficult for me to write correct grep for this, cause the names of files and directories that i am passing through are mad. Here are some of them: /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/!_1 /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/dam/$user/:e/'/-r /home/OS/pocitacove/testovaci_adresar/z/test3/skusime/ taketo/ taketo /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/.-bla/.-bla/.a=b /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/.-bla/.-bla/@ /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/.-bla/.-bla/: /home/OS/pocitacove/testovaci_adresar/z/test4.pre_expertov/.-bla/.-bla/'ano' foreach paths ($something:q) set name = "$paths:t" @ number = (`grep -Ec "$name" "$paths"`) if ($number != 0) then echo -n "$paths " echo $number endif @ number = 0 end

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  • unexpected result from gnu sort

    - by funkycat
    when I try to sort the following text file 'input': test1 3 test3 2 test 4 with the command sort input the output is exactly the input. Here is the output of od -bc input : 0000000 164 145 163 164 061 011 063 012 164 145 163 164 063 011 062 012 t e s t 1 \t 3 \n t e s t 3 \t 2 \n 0000020 164 145 163 164 011 064 012 t e s t \t 4 \n 0000027 It's just a tab separated file with two columns. When I do sort -k 2 The output changes to test3 2 test1 3 test 4 which is what I would expect. But if I do sort -k 1 nothing changes with respect to the input, whereas I would expect 'test' to sort before 'test1'. Finally, if I do cat input | cut -f 1 | sort I get test test1 test3 as expected. Is there a logical explanation for this? What exactly is sort supposed to do by default, something like: sort -k 1 ? My version of sort: sort (GNU coreutils) 7.4

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  • scp command with alert message

    - by muruga
    I want to get the alert message for every execution of the scp command. If some one access my file using the scp command, that time I have to receive one mail. How can I achieve this. Please help me.

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  • Formatting with echo command

    - by johannix
    The actual situation is a bit complicated, but the issue I'm running into is that I have an echo command within an eval command. Like so: $ eval echo 'keep my spacing' keep my spacing $ echo 'keep my spacing' keep my spacing I was wondering how I could keep eval from stripping my spacing so that the first command prints out the same message as the second...

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  • How to determine what user and group a Python script is running as?

    - by Chirael
    I have a CGI script that is getting an "IOError: [Errno 13] Permission denied" error in the stack trace in the web server's error log. As part of debugging this problem, I'd like to add a little bit of code to the script to print the user and (especially) group that the script is running as, into the error log (presumably STDERR). I know I can just print the values to sys.stderr, but how do I figure out what user and group the script is running as? (I'm particularly interested in the group, so the $USER environment variable won't help; the CGI script has the setgid bit set so it should be running as group "list" instead of the web server's "www-data" - but I need code to see if that's actually happening.)

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  • $where in mongodb web shell not working

    - by Bravo
    i have the below set of test documents which i inserted in to the mongodb and when i use to query the db using the $where get the below exception Error: database error: $where query, but no script engine Any idea why the $where clause not working test data : db.things.save({ "_id" : 1, "domainName" : "test11.com", "hosting" : "hostgator.com" }) db.things.save({ "_id" : 2, "domainName" : "test2.com", "hosting" : "aws.amazon.com"}) db.things.save({ "_id" : 3, "domainName" : "test3.com", "hosting" : "aws.amazon.com" }) db.things.save({ "_id" : 4, "domainName" : "test4.com", "hosting" : "hostgator.com" }) db.things.save({ "_id" : 5, "domainName" : "test5.com", "hosting" : "aws.amazon.com" }) db.things.save({ "_id" : 6, "domainName" : "test6.com", "hosting" : "cloud.google.com" }) db.things.save({ "_id" : 7, "domainName" : "test7.com", "hosting" : "aws.amazon.com" }) db.things.save({ "_id" : 8, "domainName" : "test8.com", "hosting" : "hostgator.com" }) db.things.save({ "_id" : 9, "domainName" : "test9.com", "hosting" : "cloud.google.com" }) db.things.save({ "_id" : 10, "domainName" : "test10.com", "hosting" : "godaddy.com" }) query used : db.things.find( { $where: "this.domainName == 'test11.com'" } );

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  • C socket programming: client send() but server select() doesn't see it

    - by Fantastic Fourier
    Hey all, I have a server and a client running on two different machines where the client send()s but the server doesn't seem to receive the message. The server employs select() to monitor sockets for any incoming connections/messages. I can see that when the server accepts a new connection, it updates the fd_set array but always returns 0 despite the client send() messages. The connection is TCP and the machines are separated by like one router so dropping packets are highly unlikely. I have a feeling that it's not select() but perhaps send()/sendto() from client that may be the problem but I'm not sure how to go about localizing the problem area. while(1) { readset = info->read_set; ready = select(info->max_fd+1, &readset, NULL, NULL, &timeout); } above is the server side code where the server has a thread that runs select() indefinitely. rv = connect(sockfd, (struct sockaddr *) &server_address, sizeof(server_address)); printf("rv = %i\n", rv); if (rv < 0) { printf("MAIN: ERROR connect() %i: %s\n", errno, strerror(errno)); exit(1); } else printf("connected\n"); sleep(3); char * somemsg = "is this working yet?\0"; rv = send(sockfd, somemsg, sizeof(somemsg), NULL); if (rv < 0) printf("MAIN: ERROR send() %i: %s\n", errno, strerror(errno)); printf("MAIN: rv is %i\n", rv); rv = sendto(sockfd, somemsg, sizeof(somemsg), NULL, &server_address, sizeof(server_address)); if (rv < 0) printf("MAIN: ERROR sendto() %i: %s\n", errno, strerror(errno)); printf("MAIN: rv is %i\n", rv); and this is the client side where it connects and sends messages and returns connected MAIN: rv is 4 MAIN: rv is 4 any comments or insightful insights are appreciated.

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  • undo continually vi

    - by wowrt
    Hi, I am using vi(not Vim) and I would like to continually undo the changes made. u works for a single command undo and Ufor a single line undo. But Is there a way to undo continuously like vim(I recall a command in vim can even undo changes by time!) in vi? Thanks in Advance.

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  • What benefits can Java developer have from moving to a *NIX platform?

    - by dave-keiture
    Hi everyone, A friend of mine is a Java developer, who's using *NIX for ages. He claims that *NIX is for real Java geeks, whereas WIN is for dummies (and I'm one of them, according to him) and girls. When I ask him to argue his position, and explain, what's so good for Java developer on *NIX, he starts talking about console, wget, curl and grep. But sorry, wget and curl analogues exist for the WIN platform as well. As for the console - I'm using FAR Commander, and have access to the command line when I need. Moreover, even if I decide moving to *NIX, I will certainly use Netbeans or Eclipse on it, so there will be no big difference. Guys, who use Java on *NIX, could you please give me some real killer examples, when *NIX (any util or technique) dramatically increases Java development productivity (in the way the hints are given in "The Pragmatic Programmer"), or, which is also important, gives more fun from the process. Thanks in advance!

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  • Different standard streams per POSIX thread

    - by Roman Nikitchenko
    Is there any possibility to achieve different redirections for standard output like printf(3) for different POSIX thread? What about standard input? I have lot of code based on standard input/output and I only can separate this code into different POSIX thread, not process. Linux operation system, C standard library. I know I can refactor code to replace printf() to fprintf() and further in this style. But in this case I need to provide some kind of context which old code doesn't have. So doesn't anybody have better idea (look into code below)? #include <pthread.h> #include <stdio.h> void* different_thread(void*) { // Something to redirect standard output which doesn't affect main thread. // ... // printf() shall go to different stream. printf("subthread test\n"); return NULL; } int main() { pthread_t id; pthread_create(&id, NULL, different_thread, NULL); // In main thread things should be printed normally... printf("main thread test\n"); pthread_join(id, NULL); return 0; }

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  • URL protocol handler shell execute problem

    - by Chuck
    Hi, I'm working on a small hobby web site where I'm able to launch a local app with certain arguments based on links. Setting up a protocol wasn't difficult, as described in http://msdn.microsoft.com/en-us/library/aa767914(VS.85).aspx, but I have one dilemma: Let's say the protocol is: foo:127.0.0.1:1111, so a link like href="foo:127.0.0.1:1111" would launch an app like: bar.exe "%1". Since I don't have any control over bar.exe (if I had, then it would be no problem to just parse it, obviously), I need some help parsing %1. bar.exe will launch correctly if it's run as bar.exe 127.0.0.1:1111, but not if it's run as bar.exe foo:127.0.0.1:1111. So I guess my question is... is there ANY way to tell the registry to pass on not %1, but a trimmed %1? (Thinking in terms of regexp where you have match[0] = all of the matched, match[1] = first capture in the matched text). I can solve it by having a .bat instead of .exe, but as I would like to make it as easy as possible for the user to use, I would LOVE it if I could handle it all stricly in registry. Any help is greatly appreciated! Chuck

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  • Checking status after wait()

    - by Helper Method
    After creating a child process and exiting it immediately (_exit()), I want to perform a wait and check the status. Now I wonder if in the 'else' branch of the if/else construct I also need to check for WIFSIGNALED. As far as I understand, if I perform a wait, a) an error could have occured (-1), the child could have terminated normally by an (exit() or _exit()), or it could have been terminated by a signal, so the check could be omitted, right? //remainder omitted int status; pid_t t_pid = wait(&status); if (t_pid == -1) { perror("wait"); exit(EXIT_FAILURE); } if (WIFEXITED(status)) { printf("child terminated normally, status = %d\n", WEXITSTATUS(status) ); } else { // <-- do it have to check for WIFSIGNALED() here? printf("child was terminated by a signal, signum = %d\n", WTERMSIG(status) ); }

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  • Bash Script using Grep to search for a pattern in a file

    - by atif089
    I am writing a bash script to search for a pattern in a file using GREP. I am clueless for why it isnt working. This is the program echo "Enter file name..."; read fname; echo "Enter the search pattern"; read pattern if [ -f $fname ]; then result=`grep -i '$pattern' $fname` echo $result; fi Or is there different approach to do this ? Thanks

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  • BASH: How to remove all files except those named in a manifest?

    - by brice
    I have a manifest file which is just a list of newline separated filenames. How can I remove all files that are not named in the manifest from a folder? I've tried to build a find ./ ! -name "filename" command dynamically: command="find ./ ! -name \"MANIFEST\" " for line in `cat MANIFEST`; do command=${command}"! -name \"${line}\" " done command=${command} -exec echo {} \; $command But the files remain. [Note:] I know this uses echo. I want to check what my command does before using it.

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