Yes, I did. Thanks!

Here is the code I use for parsing the CSV file:

#! /usr/local/bin/perl 
#
#script opens and parses a CSV file,
#removes carriage return
#and writes all into a new text file
#
#tested:  --ok!

use strict;
use warnings;
use Text::CSV;


 #Input CSV filename
 my $file = $ARGV[0];
 
 if (!$ARGV[0]) {
 $file = './data/IDs_test.csv'; #Default
 }
 
 if (!-f $file) {
 print "Can not find $file: $!\n";
 exit 1;
 }
 
 #Parsing CSV
 local $/ = "\r\n";        #add windows carriage return to perl's eol 
+(newline)
 
 my $csv = Text::CSV ->new ({binary =>1, eol => $/});
 
 open (my $fhCSV, '<', $file) or die "Can not open $file: $!\n";
 open (my $fhOUT, '>', './data/IDs.txt') or die "Can not open: $!\n";
 
 while (my $line = <$fhCSV>) {
        if ($csv->parse($line)) {
        my @fields = $csv->fields ();
        chomp (@fields);
        print $fhOUT "@fields\n";
        }
        else {
        warn "Line could not be parsed: $line\n";
        }
 }
 print "CSV parsed and saved as text file: /data/IDs.txt!";
 close $fhCSV;
 close $fhOUT;
[download]

Try this.

$id =~ s/([a-z]) ([a-z])/$1,$2/;
[download]

Marvellous!

Thanks a lot!

It works!

But,oops, I found a few exceptions, like: A B 1234 a c d

I tried to fix this by simply extending your script:

$id =~ s/([a-z]) ([a-z]) ([a-z])/$1,$2,$3/;

But this doesn't work!

better

Oh yes, it does!

I just swaped both lines, so that the extended line preceeds your line. And voilą!

There are a number of ways to craft a regular expression to do this. One is to use look-behind and look-ahead assertions. These make sure the characters surrounding the space character match, but will leave them alone and not include them in the text to be replaced:

$id =~ s/(?<=[a-z]) (?=[a-z])/,/;
[download]

However, the results of any regex are likely to be spotty. If instead you use a module like Text::CSV to parse your csv files, you should be able to receive your data clean with all commas intact

If the sample data are exactly as you posted them (hard to tell since you didn't use code tags),

 A B 1234 a,b -> ...
A B 1234 c,e -> ....
[download]

then it appears to me that you are dealing NOT with CSV. but rather, with SPACE-SEPARATED values (or, perhaps TSV if something in the writeup process transformed tabs to single spaces). If that's the case, you can't solve your problem by treating the data as if it were comma-separated.

OTOH (and again presuming that the OP reflects the data precisely), could this actually be CSV data with just two fields?

Well, I parsed variably structured strings, consisting of different characters, like: letters, numbers, space, brackets, minus, comma from a CSV file.

The CSV file is a database output in the form of an Excel worksheet, saved as a CSV file. The first coloumn contains fields with a series of letters and numbers, called IDs, i.e.

|A B 1234 a <1>|
|A B 1234 a,b|
[download]

In order to look up the image files corresponding to the IDs, I parse the IDs of the CSV file into a text file, which will later be opened as a file handle. During the parsing of the IDs the comma of comma separated letters (like: a,b or c,e) which are part of the ID is accidentally (?) deleted.

Just to point out the context: The parsing is the first step of a file import, see nodes:

Read text file - Encoding problem?

Looking up elements of an array in another array!

Now you know how to avoid the problem :)(look around Parse CSV stream, be forgiving on bad lines ) Use Text::CSV or Text::xSV

Examples at

• join - join two files according to a common key
• part - split up files according to column value
• Merge two files with similar column entries
• Opening multiple files ( csvpaste.pl )
• Open multiple file handles?
• X, Y Table structure
• How to extract the particular residues from PDB files(text csv split hash bioperl)
• Select only desired features from a text (text csv split hash bioperl)
• Sort on Table headers (text csv split hash bioperl)
• I need help joining tab-delimited files/tables!
• split then join based on common value in field
• Smart way to read a file vertically?
• reformatting tab delimited file
• edit a CSV and "in-place" replacement
• Re: Reversing a mysql table, transpose-tsv -- invert a tab-delimited table

• Text::CSV

  examples/csv2xls	Script to onvert CSV files to M$Excel
  examples/csv-check	Script to check a CSV file/stream
  examples/csvdiff	Script to shoff diff between sorted CSV files
  examples/parser-xs.pl	Parse CSV stream, be forgiving on bad lines

merging csv files into a third file preserving column & row

Hello again, Anonymous Monk!

Thanks a lot for your extensive response!

I'm fighting not to get buried in this avalanche of wisdom ;-)

Seriously, I appreciate your help, which seems to guide me through my whole project.

I can find already hints in your list of links for the next step: parsing a CSV into a hash, which I will need for tagging the image files, I imported before (s. my node:

Looking up elements of an array in another array!

better