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Full Discussion: How to read a file, line by line in UNIX script?
Top Forums Shell Programming and Scripting How to read a file, line by line in UNIX script? Post 302880404 by Yoda on Thursday 19th of December 2013 11:29:44 AM
Old 12-19-2013
It is definitely reading that file, but you cannot reference a shell variable inside an awk code by using dollar sign. So below statement in awk code is wrong:
Code:
if($1=="$file" && $4 != "")

You should assign a shell variable to awk variable using -v option and use it instead.

Also that for loop syntax is not recommended

I would suggest you to post your input and expected output and someone in this forum can suggest you a better approach.
 

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LEARN ABOUT DEBIAN

bp_dbsplit

BP_DBSPLIT(1p)						User Contributed Perl Documentation					    BP_DBSPLIT(1p)

NAME

       dbsplit - script to split an input set of database(s) into smaller pieces

SYNOPSIS

	 dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat]
		     [--prefix outputprefix] [ < file1 file 2  OR file1 file2]

DESCRIPTION

       This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate
       files of X numbers of sequences.  You specify X with the "--size/-s" parameter.	The input and output sequence format is any that is
       supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc).

       You can specify the input data either as a single file with -i filename, or as a single file as an argument like

	 % dbsplit file1 file2

       or as a list of sequence data with

	 % cat file1 file2 file3 | dbsplit

       You'll want to use the "--prefix" to specify what the output prefix will be.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02							    BP_DBSPLIT(1p)
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