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  • sed find pattern on line with another pattern

    - by user2962390
    I am trying to extract text from a file between a '<' and a '', but only on a line starting with another specific pattern. So in a file that looks like: XXX Something here XXX Something more here XXX <\Lines like this are a problem ZZZ something <\This is the text I need XXX Don't need any of this I would like to print only the "<\This is the text I need". If I do sed -n '/^ZZZ/p' FILENAME it pulls the correct lines I need to look at, but obviously prints the whole line. sed -n '/</,//p' FILENAME prints way too much. I have looked into grouping and tried sed -n '/^ZZZ/{/</,//} FILENAME but this doesn't seem to work at all. Any suggestions? They will be much appreciated. (Apologies for formatting, never posted on here before)

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  • finding empty directories unix

    - by soField
    i need to find empty directories for given list of directories some directories have directories inside it if inside directories also empty i can say main directory is empty otherwise it's not empty how can i test this for example A>A1(file1),A2 this is not empty beacuse of file1 B>B1(no file) this is empty C>C1,C2 this is empty thanks

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  • Uniq in awk; removing duplicate values in a column using awk

    - by D W
    I have a large datafile in the following format below: ENST00000371026 WDR78,WDR78,WDR78, WD repeat domain 78 isoform 1,WD repeat domain 78 isoform 1,WD repeat domain 78 isoform 2, ENST00000371023 WDR32 WD repeat domain 32 isoform 2 ENST00000400908 RERE,KIAA0458, atrophin-1 like protein isoform a,Homo sapiens mRNA for KIAA0458 protein, partial cds., The columns are tab separated. Multiple values within columns are comma separated. I would like to remove the duplicate values in the second column to result in something like this: ENST00000371026 WDR78 WD repeat domain 78 isoform 1,WD repeat domain 78 isoform 1,WD repeat domain 78 isoform 2, ENST00000371023 WDR32 WD repeat domain 32 isoform 2 ENST00000400908 RERE,KIAA0458 atrophin-1 like protein isoform a,Homo sapiens mRNA for KIAA0458 protein, partial cds., I tried the following code below but it doesn't seem to remove the duplicate values. awk ' BEGIN { FS="\t" } ; { split($2, valueArray,","); j=0; for (i in valueArray) { if (!( valueArray[i] in duplicateArray)) { duplicateArray[j] = valueArray[i]; j++; } }; printf $1 "\t"; for (j in duplicateArray) { if (duplicateArray[j]) { printf duplicateArray[j] ","; } } printf "\t"; print $3 }' knownGeneFromUCSC.txt How can I remove the duplicates in column 2 correctly?

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  • How to line up columns using paste(1)? or how to make an aligned table merging lines in the shell?

    - by nn
    Hi, I want to merge lines such that the merged lines are aligned on the same boundary. UNIX paste(1) does this nicely when lines all meet at the same tab boundary, but when lines differ in size (in the file that lines are being merged into), the text comes out awkward. Example of paste(1) that has the desired effect: $ echo -e "a\nb\nccc\nd" | paste - - a b ccc d Example of paste(1) with undesired effect: $ echo -e "a\nb\ncccccccccccc\nd" | paste - - a b cccccccccccc d Note how the 2nd column doesn't line up. I want 'b' to line up with 'd', which requires an additional tab. Unfortunately I believe this is the limit for the paste utility, so if anyone has any idea of how to get the desired effect above, I'd love to hear it.

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  • Appending rather than overwriting files when moving

    - by ukas1
    I have the following directory structure: +-archive +-a +-data.txt +-b +-data.txt +-incoming +-a +-data.txt +-c +-data.txt How do I do the equivalent of mv incoming/* archive/ but have the contents of the files in incoming appended to those in archive rather than overwrite them?

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  • symlink files newer than X age, then later remove symlink once file ages?

    - by bleomycin
    Hello everyone, i have a large number of files/folders coming in each day that are being sorted automatically to a wide variety of folders. I'm looking for a way to automatically find these files/folders and create symlinks to them all within an "incoming" folder. Searching for file age should be sufficient for finding the files, however searching for age and owner would be ideal. Then once the files/folders being linked to reach a certain age, say 5 days, remove the symlinks to them automatically from the "incoming" folder. Is this possible to do with a simple shell or python script that can be run with cron? Thanks!

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  • UNIX Programs (Shell Scripting) [closed]

    - by atif089
    Hi, I have an exam tomorrow and I need some help with these programs. Or if you can tell me where I can get these. Write a program which uses grep to search a file for a pattern and display search patterns on standard output Write an awk program to print only odd numbered lines of a file. Write a program to open the command ls and give the output to the command through which we count the number of files Thank You :)

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  • Word frequency tally script is too slow

    - by Dave Jarvis
    Background Created a script to count the frequency of words in a plain text file. The script performs the following steps: Count the frequency of words from a corpus. Retain each word in the corpus found in a dictionary. Create a comma-separated file of the frequencies. The script is at: http://pastebin.com/VAZdeKXs Problem The following lines continually cycle through the dictionary to match words: for i in $(awk '{if( $2 ) print $2}' frequency.txt); do grep -m 1 ^$i\$ dictionary.txt >> corpus-lexicon.txt; done It works, but it is slow because it is scanning the words it found to remove any that are not in the dictionary. The code performs this task by scanning the dictionary for every single word. (The -m 1 parameter stops the scan when the match is found.) Question How would you optimize the script so that the dictionary is not scanned from start to finish for every single word? The majority of the words will not be in the dictionary. Thank you!

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  • How to remove all words written in capital letters ONLY (by using sed and/or awk)

    - by Virtual_Lotos
    I am trying to delete all words written in capital letters only by using sed: sed -r "s/\b[A-Z]\w*\s*//g" < file1 > file2 But this solution capture all the words starting with capital letters and delete them (this in not the goal). Here's an example: file1 content: AAAAAAAAAAAA BBbbbbb AbAbAbAb aaaaaBBBBB AAAAAA BBBBBB A1-B1 a1-b1 A1-b1 AA AAAAA BBBBB AAAAA Abbbb AAA AAAAA AAAABB Abbbb Baaaa Aaaaa AB AAAAAA1 BBBBBBb AAAAAA 1 BBBBBB b Result should be like this (file2 content): BBbbbbb AbAbAbAb aaaaaBBBBB A1-B1 a1-b1 A1-b1 AA Abbbb AAA Abbbb Baaaa Aaaaa AB AAAAAA1 BBBBBBb AAAAAA 1 BBBBBB b Each line of at least one digit or one lowercase letter should remain intact (should not be deleted).

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  • Random password variable disappears

    - by snaken
    Hi, I'm using the following to generate a random password in a shell script: DBPASS=</dev/urandom tr -dc A-Za-z0-9| (head -c $1 > /dev/null 2>&1 || head -c 8) When i run this in a file on its own like this: #!/bin/sh DBPASS=</dev/urandom tr -dc A-Za-z0-9| (head -c $1 > /dev/null 2>&1 || head -c 8) echo $DBPASS A password is echoed. When i incorporate it into a larger script though the variable never seems to get created for some reason, so for example this doesn't work: DBPASS=</dev/urandom tr -dc A-Za-z0-9| (head -c $1 > /dev/null 2>&1 || head -c 8) sed -i s/oldpass/$DBPASS/ mysql_connect.php If i manually set the variable though everything is fine.. can anyone see why?

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  • find: What's up with basename and dirname?

    - by temp2290
    I'm using find for a task and I noticed that when I do something like this: find `pwd` -name "file.ext" -exec echo $(dirname {}) \; it will give you dots only for each match. When you s/dirname/basename in that command you get the full pathnames. Am I screwing something up here or is this expected behavior? I'm used to basename giving you the name of the file (in this case "file.ext") and dirname giving you the rest of the path.

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  • Notify via email if something wrong got happened in the shell script

    - by Nevzz03
    fileexist=0 for i in $( ls /data/read-only/clv/daily/Finished-HADOOP_EXPORT_&processDate#.done); do mv /data/read-only/clv/daily/Finished-HADOOP_EXPORT_&processDate#.done /data/read-only/clv/daily/archieve-wip/ fileexist=1 done --some other script below Above is the shell script I have in which in the for loop, I am moving some files. I want to notify myself via email if something wrong got happened in the moving process, as I am running this script on the Hadoop Cluster, so it might be possible that cluster went down while this was running etc etc. So how can I have better error handling mechanism in this shell script? Any thoughts?

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  • What is common between environments within a shell terminal session?

    - by Matt1776
    I have a custom shell script that runs each time a user logs in or identity is assumed, its been placed in /etc/profile.d and performs some basic env variable operations. Recently I added some code so that if screen is running it will reattach it without needing me to type anything. There are some problems however. If I log-in as root, and su - to another user, the code runs a second time. Is there a variable I can set when the code runs the first time that will prevent a second run of the code? I thought to write something to the disk but then I dont want to prevent the code from running if I begin a new terminal session. Here is the code in question. It first attempts to reattach - if unsuccessful because its already attached (as it might be on an interruped session) it will 'take' the session back. screen -r if [ -z "$STY" ]; then exec screen -dR fi Ultimately this bug prevents me from substituting user to another user because as soon as I do so, it grabs the screen session and puts me right back where I started. Pretty frustrating

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  • How do I conditionally redirect the output of a command to /dev/null?

    - by Lawrence Johnston
    I have a script. I would like to give this script a quiet mode and a verbose mode. This is the equivalent of: if $verbose then redirect="> /dev/null" fi echo "Verbose mode enabled" $redirect # This doesn't work because the redirect isn't evaluated. I'd really like a better way of doing this than writing if-elses for every statement affected. eval could work, but has obvious side effects on other variables.

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  • Shell Script Variable Quoting Problem

    - by apinstein
    I have an sh script that contains the line $PHP_COMMAND -r 'echo get_include_path();' I can not edit this script, but I need the eventual command line to be (equivalent to) php -d include_path='/path/with spaces/dir' -r 'echo get_include_path();' How can I achieve this? Below is a script that demonstrates the problem. #!/bin/sh # shell script quoting problem demonstration # I need to be able to set a shell variable with a command with # some options, like so PHP_COMMAND="php -d 'include_path=/path/with spaces/dir'" # then use PHP_COMMAND to run something in another script, like this: $PHP_COMMAND -r 'echo get_include_path();' # the above fails when executed. However, if you copy/paste the output # from this line and run it in the CLI, it works! echo "$PHP_COMMAND -r 'echo get_include_path();'" php -d include_path='/path/with spaces/dir' -r 'echo get_include_path();' # what's going on? # this is also interesting echo "\n--------------------" # this works great, but only works if include_path doesn't need quoting PHP_COMMAND="php -d include_path=/path/to/dir" echo "$PHP_COMMAND -r 'echo get_include_path();'" $PHP_COMMAND -r 'echo get_include_path();' echo "\n--------------------" # this one doesn't when run in the sh script, but again if you copy/paste # the output it does work as expected. PHP_COMMAND="php -d 'include_path=/path/to/dir'" echo "$PHP_COMMAND -r 'echo get_include_path();'" $PHP_COMMAND -r 'echo get_include_path();' Script also available online: http://gist.github.com/276500

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  • Parsing result of Diff in Shell Script

    - by Saobi
    I want to compare two files and see if they are the same or not in my shell script, my way is: diff_output=`diff ${dest_file} ${source_file}` if [ some_other_condition -o ${diff_output} -o some_other_condition2 ] then .... fi Basically, if they are the same ${diff_output} should contain nothing and the above test would evaluate to true. But when I run my script, it says [: too many arguments On the if [....] line. Any ideas?

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  • Save JSON outputed from a URL to a file

    - by Aidan
    Hey Guys, How would I save JSON outputed by an URL to a file? e.g from the Twitter search API (this http://search.twitter.com/search.json?q=hi) Language isn't important. Thanks! edit // How would I then append further updates to EOF?

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  • Sed-replacing a pattern

    - by grails_enthu
    I have below code: <td nowrap="nowrap" width="74"> <p align="center">server1</p> </td> <td nowrap="nowrap" width="74"> <p align="center">server2</p> </td> and so on.I want to get output as: <td nowrap="nowrap" width="74">server1</td> <td nowrap="nowrap" width="74">server2</td> What should be my approach?Say for example the file is server.html I have done something like this: sed "s/<p align="center">*</p>/*/" -i server.html But its not working.

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  • Import files directly to SVN repo without checking out first

    - by Werner
    Hi, I am using SVN and have a repository on a remote machine. Sometimes, when working on my local machine I realize that I need to add some new files to the repo. The usual procedure I know would then be: 1- at the current folder on my local machine checkout the whole SVN repo 2- enter there 3- copy the interesting file here 4- commit But this can be a bit tedious. I wonder if somehow, I can omit steps 1 to 3 and import the "interesting" file to SVN directly without necessity of checking out the repo first. Thanks

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  • How to write a program that mimics Fiddler by using tcpdump or from scratch?

    - by ????
    When Fiddler is not on Mac OS X or Ubuntu, and if we don't install/use Wireshark or any other more heavy duty tools, what is a way to use tcpdump so that 1) It can print out GET /foo/bar HTTP/1.1 [request content in RAW text] [response content in RAW text] POST /foo/... HTTP/1.1 this should be able to be done by tcpdump or by using tcpdump in a short shell script or Ruby / Python / Perl script. 2) Actually, it can be neat if a script can output HTML, with GET /foo/bar HTTP/1.1 POST /foo/... HTTP/1.1 on the page, for any browser to display, and then when clicked on any of those lines, it will expand to show the RAW content like (1) above does. Click again and it will hide the details. The expansion UI can be done using jQuery or any JS library. The script may be short... possibly less than 20 lines? Does anybody know how to do it either for (1) or (2)?

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  • Linux: programatically setting a permanent environment variable

    - by Richard
    Hello All, I am writing a little install script for some software. All it does is unpack a target tar, and then i want to permanently set some environment variables - principally the location of the unpacked libs and updating $PATH. Do I need to programmatically edit the .bashrc file, adding the appropriate entries to the end for example, or is there another way? What's standard practice? Thanks

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  • Is there a way to set the value of $? in a mock in Ruby?

    - by rleber
    I am testing some scripts that interface with system commands. Their logic depends on the return code of the system commands, i.e. the value of $?. So, as a simplified example, the script might say: def foo(command) output=`#{command}` if $?==0 'succeeded' else 'failed' end end In order to be able to test these methods properly, I would like to be able to stub out the Kernel backquote call, and set $? to an arbitrary value, to see if I get appropriate behavior from the logic in the method after the backquote call. I can't figure out a way to do this. (In case it matters, I'm testing using Test::Unit and Mocha.)

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