"I used your example and added file references but the script is not outputting all of the rows."

You haven't shown any input or output!

I am unable to reproduce your problem using your code above (with just the filenames changed). My script (pm_csv_to_psv_fhs.pl) has:

my $FileIn = './pm_csv_to_psv_fhs.in';
my $FileOut = './pm_csv_to_psv_fhs.out';
[download]

Here's a verbatim run showing input and (before and after) output:

ken@ganymede: ~/tmp
$ cat pm_csv_to_psv_fhs.in
a,b,"c,d",e
"f,g,h",i,j,"k,l"
m,n,o,p,q,r,s,t
"u,v,w,x,y,z"
ken@ganymede: ~/tmp
$ cat pm_csv_to_psv_fhs.out
cat: pm_csv_to_psv_fhs.out: No such file or directory
ken@ganymede: ~/tmp
$ pm_csv_to_psv_fhs.pl
ken@ganymede: ~/tmp
$ cat pm_csv_to_psv_fhs.out
a|b|c,d|e
f,g,h|i|j|k,l
m|n|o|p|q|r|s|t
u,v,w,x,y,z
ken@ganymede: ~/tmp
$
[download]

Please show equivalent information for a run of your script.

Here's some other points to consider: all documented in open.

• Check if you're successfully opening the files: open ... or die "Can't open ...: $!";
• You've used the recommended 3-argument form for the input file. Why not for the output file?
• The mode for the output file is '+>'. Why? Perhaps you wanted append mode ('>>') or read-write mode without clobbering the file first ('+<').
• You only show code for writing to the output file. If you really do want read-write mode, where's the code for the reading part?

Given you're new to Perl, you may be finding the documentation for open to be a little heavy going. If so, read perlopentut first - it provides a gentler introduction to the subject.

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