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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

09-14-2011

Registered User

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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LEARN ABOUT PLAN9

zgrep

ZGREP(1)						      General Commands Manual							  ZGREP(1)

NAME

       zgrep - search possibly compressed files for a regular expression

SYNOPSIS

       zgrep [ grep_options ] [ -e ] pattern filename...

DESCRIPTION

       Zgrep  invokes  grep  on  compressed  or  gzipped  files.   These  grep	options  will  cause  zgrep  to  terminate  with  an  error  code:
       (-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*).  All other options specified are passed directly to grep.  If no file is specified,  then  the
       standard input is decompressed if necessary and fed to grep.  Otherwise the given files are uncompressed if necessary and fed to grep.

       If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.

EXIT CODE

       2 - An option that is not supported was specified.

AUTHOR

       Charles Levert (charles@comm.polymtl.ca)

SEE ALSO

       grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)

																	  ZGREP(1)

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