Although you CAN use simple greps to get things, I would advise the use of http://www.bioperl.org/wiki/HOWTO:SeqIO It understands the Standard Chromatogram Format (SCF) and can grab exactly what you will ever need. 

use Bio::SeqIO;

$in = new Bio::SeqIO -file => 'p122.gel', -format=>'SCF';
$seq = $in->next_seq();

# if you want to look at the various comment field data:
while ( ($key, $val) = each %{$seq->names()} ) {
    print "$key\t$val\n";
}

[download]

If this is just your Computer Science homework, then you should do proper investigation first (i.e. learn), instead of asking us. For example, the SCF format is: 

 SCF Done:  E(RHF) =  -113.873389817     A.U. after   11 
cycles
/SCF Done.*=\s?([\-\d\.]*\d+)/

[download]

Perl uses regular expressions that are very precise, hence, the suggestion it would look like: 

 SCF Done=  -113.873389817.
/SCF Done=\s?([\-\d\.]*\d+)/

[download]

Would, in the eyes of Perl, make it totally different. Where the first line is the line of the SCF file, and the second a Perl patternmatch that will grab that part. You can see differences... 

perl -ne '$V{$1}=$ARGV if /SCF Done.*=\s*([\-\d\.]*\d+)/; END{@_=sort 
+keys %V;print "Lowest value is $_[0] in file $V{$_[0]}\n"}'  *.log

[download]

So, the big question is still: We can help, but only if you make an effort, and show us what you have up to this point. Do you have a loop, which variables are you going to use. Will you use a single or a double pass over the files. How do you think that 3th column should be retrieved, etc. Show us some code first.

In reply to Re: Making commond for large number of files by FreeBeerReekingMonk
in thread Making commond for large number of files by acrobat118

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