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Top Forums Shell Programming and Scripting Help with generating a script Post 302555109 by kellywilliams on Wednesday 14th of September 2011 12:49:38 AM
Old 09-14-2011
Help with generating a script

I am a biologist who is new to linux and am having difficulty generating a script to do what I want it to do! I have tried basic grep commands, but even that does not give me back the data I want.

I have many files that are all currently in .xslx and I'm not sure if they need to be .csv or .txt for this to work... Each of these files has ~90,000 lines.

Basically I want a script that will ask me what I am looking for:
Code:
echo Please input gene name you wish to look for
read GeneName

Then I want to look through all of the lines in all of my files (~200) and see if $GeneName is present in field 13 (it may be present multiple times in the one file, or not at all).

If it is present in field 13, I want the entire line/s it is in, plus the file name/s it is found in to be printed to a .txt file.

I have tried using grep command and it just gives me back all lines from the file, not the lines containing $GeneName. I apologise I do not have a better unix background, but I have been trying for days and I just cannot generate it!!! I would appreciate any help.

Kelly
 

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NPM-RUN-SCRIPT(1)														 NPM-RUN-SCRIPT(1)

NAME
npm-run-script - Run arbitrary package scripts SYNOPSIS
npm run-script <command> [--silent] [-- <args>...] alias: npm run DESCRIPTION
This runs an arbitrary command from a package's "scripts" object. If no "command" is provided, it will list the available scripts. run[-script] is used by the test, start, restart, and stop commands, but can be called directly, as well. When the scripts in the package are printed out, they're separated into lifecycle (test, start, restart) and directly-run scripts. As of ` https://blog.npmjs.org/post/98131109725/npm-2-0-0, you can use custom arguments when executing scripts. The special option -- is used by getopt https://goo.gl/KxMmtG to delimit the end of the options. npm will pass all the arguments after the -- directly to your script: npm run test -- --grep="pattern" The arguments will only be passed to the script specified after npm run and not to any pre or post script. The env script is a special built-in command that can be used to list environment variables that will be available to the script at run- time. If an "env" command is defined in your package, it will take precedence over the built-in. In addition to the shell's pre-existing PATH, npm run adds node_modules/.bin to the PATH provided to scripts. Any binaries provided by locally-installed dependencies can be used without the node_modules/.bin prefix. For example, if there is a devDependency on tap in your package, you should write: "scripts": {"test": "tap test/*.js"} instead of "scripts": {"test": "node_modules/.bin/tap test/*.js"} to run your tests. The actual shell your script is run within is platform dependent. By default, on Unix-like systems it is the /bin/sh command, on Windows it is the cmd.exe. The actual shell referred to by /bin/sh also depends on the system. As of ` https://github.com/npm/npm/releases/tag/v5.1.0 you can customize the shell with the script-shell configuration. Scripts are run from the root of the module, regardless of what your current working directory is when you call npm run. If you want your script to use different behavior based on what subdirectory you're in, you can use the INIT_CWD environment variable, which holds the full path you were in when you ran npm run. npm run sets the NODE environment variable to the node executable with which npm is executed. Also, if the --scripts-prepend-node-path is passed, the directory within which node resides is added to the PATH. If --scripts-prepend-node-path=auto is passed (which has been the default in npm v3), this is only performed when that node executable is not found in the PATH. If you try to run a script without having a node_modules directory and it fails, you will be given a warning to run npm install, just in case you've forgotten. You can use the --silent flag to prevent showing npm ERR! output on error. You can use the --if-present flag to avoid exiting with a non-zero exit code when the script is undefined. This lets you run potentially undefined scripts without breaking the execution chain. SEE ALSO
o npm help 7 scripts o npm help test o npm help start o npm help restart o npm help stop o npm help 7 config January 2019 NPM-RUN-SCRIPT(1)
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