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Full Discussion: Problem using grep in bash script
Top Forums Shell Programming and Scripting Problem using grep in bash script Post 302565241 by errcricket on Monday 17th of October 2011 10:59:35 AM
Old 10-17-2011
searching files using grep command in bash script
When it comes to programing and UNIX, I know just enough to be really really dangerous.

I have written a python script to parse through a file that contains ~1 million lines. Depending on whether a certain string is matched, the line is copied into a particular file. For the sake of brevity, the lines are something like this:

Quote:
ABC-1
ABC-1
CCC-33
CCC-33
CCC-33
...
I tried the python code out on a small file, and everything seems to work. However, since the actual file is a massive, I want to double check it with grep to make sure that the total number of ABC-1's in file x is the same number of ABC-1's in file y.

On the command line, I wrote a simple script that will check this for me.

Code:
grep "ABC-1" fileName.fna | wc -l

This seems to work just fine.

Problem: The contents of the original file are copied into 10 other files. I want check each file AND since there are ~50 unique strings (i.e. ABC-1), I would like to check for each string. Writing the simple script ~500 times is tedious.

I wrote a bash script but when I execute the file from the command line (
Quote:
bash counts.sh
), I get an error saying wc is an illegal option and that it cannot be found.

Code:
#!/bin/bash
echo "ABC-1 in fileName.fna"
grep "ABC-1" fileName.fna | wc -l

echo "CCC-33 in fileName3.fna"
grep "CCC-33" fileName3.fna | wc -l

Ideally, I think I should make a vector/list/array of file names and a vector/list/array of searchable strings and use a loop that will print out the string, the filename, and the number of times the string occurs in the file...but I don't know how to do that.

So if anyone knows how to re-arrange my 1-liner script - thank you. If anyone can help me with writing a loop script - thank you. Either option would be awesome.
Last edited by errcricket; 10-17-2011 at 12:18 PM.. Reason: better title
 

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LEARN ABOUT CENTOS

devscripts.conf

DEVSCRIPTS.CONF(5)						File Formats Manual						DEVSCRIPTS.CONF(5)

NAME

       devscripts.conf - configuration file for the devscripts package

DESCRIPTION

       The  devscripts	package provides a collection of scripts which may be of use to Debian developers and others wishing to build Debian pack-
       ages.  Many of these have options which can be configured on a system-wide and per-user basis.

       Every script in the devscripts package which makes use of values from these configuration files describes the specific settings	recognised
       in its own manpage.  (For a list of the scripts, either see /usr/share/doc/devscripts/README.gz or look at the output of dpkg -L devscripts
       | grep /usr/bin.)

       The two configuration files are /etc/devscripts.conf for system-wide defaults and ~/.devscripts for per-user settings.	They  are  written
       with  bash(1)  syntax, but should only have comments and simple variable assignments in them; they are both sourced (if present) by many of
       the devscripts scripts.	Variables corresponding to simple switches should have one of the values yes and no; any other setting is regarded
       as equivalent to the default setting.

       All  variable  names  are  written  in  uppercase, and begin with the script name.  Package-wide variables begin with "DEVSCRIPTS", and are
       listed below, as well as in the relevant manpages.

       For a list of  all  of  the  available  options	variables,  along  with  their	default  settings,  see  the  example  configuration  file
       /usr/share/doc/devscripts/devscripts.conf.ex.   This  is  copied  to  /etc/devscripts.conf  when the devscripts package is first installed.
       Information about configuration options introduced in newer versions of the package will be appended to /etc/devscripts.conf when the pack-
       age is upgraded.

       Every script which reads the configuration files can be forced to ignore them by using --no-conf as the first command-line option.

PACKAGE-WIDE VARIABLES
       The currently recognised package-wide variables are:

       DEVSCRIPTS_CHECK_DIRNAME_LEVEL, DEVSCRIPTS_CHECK_DIRNAME_REGEX
	      These  variables	control  scripts  which change directory to find a debian/changelog file or suchlike, and some other miscellaneous
	      cases.  In order to prevent unwanted, even possibly dangerous, behaviour, these variables control when actions  will  be	performed.
	      The scripts which currently make use of these variables are: debc, debchange/dch, debclean, debi, debrelease, debuild and uscan, but
	      this list may change with time (and I may not remember to update this manpage).  Please see the manpages of individual  scripts  for
	      details of the specific behaviour for each script.

SEE ALSO

       devscripts(1) and /usr/share/doc/devscripts/README.gz.

AUTHOR

       This manpage was written for the devscripts package by the package maintainer Julian Gilbey <jdg@debian.org>.

DEBIAN
								 Debian Utilities						DEVSCRIPTS.CONF(5)
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