Re: Need method to create Regular expression for known pattern in the middle of a line

This should suit your needs (it only adds the " if the pattern matches otherwise it leaves it alone.):

use strict;
use warnings;

while ( <DATA> ) {
  s/([^"])(,\w*,\w*,ResGen,)/$1"$2/;
  print;
}

__DATA__
GENE1="Rattus norvegicus serum and glucocorticoid-regulated kinase (sg
+k) mRNA, complete cds,NM_019232,333,ResGen,ATP binding|protein serine
+/threonine kinase|protein amino acid phosphorylation,,,,29517
GENE2="ESTs, Weakly similar to putative serine/threonine protein kinas
+e MAK-V [M.musculus]",NM_144755,331,ResGen,,,,,246273
GENE3="Thiosulfate sulphurtransferase (rhodanese)",X56228,329,ResGen,m
+itochondrion|sulfate transport|thiosulfate sulfurtransferase,,,,25274
GENE4="Spleen tyrosine kinase,NM_012758,327,ResGen,ATP binding|protein
+ tyrosine kinase|intracellular signaling cascade|protein amino acid p
+hosphorylation,,,,25155
GENE5="Spleen kinase 24,NM_012758,,ResGen,ATP binding|protein tyrosine
+ kinase|intracellular signaling cascade|protein amino acid phosphoryl
+ation,,,,25155
[download]

This assumes a lot from your data. Mainly that the only thing possible between the commas lie in the character class [A-Za-z0-9_]

-enlil

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Re: Re: Need method to create Regular expression for known pattern in the middle of a line by tachyon (Chancellor) on Feb 10, 2003 at 08:03 UTC
The problem with your regex (which may or may not be a real problem) is that the \w* limit what is included - a ( or \| etc will cause an aberrant failure. It would be much more robust to use `[^,]*` as this includes everything except the comma separator.... cheers tachyon s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print	[reply] [d/l]
Re: Re: Re: Need method to create Regular expression for known pattern in the middle of a line by Ya (Initiate) on Feb 10, 2003 at 08:39 UTC
I am sorry to have not mentioned this earlier that, fields may be delimited with dobule quotes only on one side and may conatin commas as part of field content. My Problem is to identify fields which were delimited only on side with double quote but may or may not have commas in them. And then to delimit them in double quotes. regards Ya	[reply]
Re: Re: Re: Re: Need method to create Regular expression for known pattern in the middle of a line by tachyon (Chancellor) on Feb 10, 2003 at 17:51 UTC
The only change you need to make to the code I suggested would be to to use Text::CSV or similar to split your CSV elements up. This will correctly deal with commas,"within, quotes,",,,and,only,split,on,the,unquoted,commas `use Text::CSV; my $csv = Text::CSV->new(); while(<DATA>) { my ($name, $data) = split "="; $csv->parse($data); my @data = $csv->fields(); for my $i ( 0.. $#data ) { next unless $data[$i] eq 'ResGen'; # found a ResGen so see what we had 3 commas ago (do bounds chec +k to0) next if $i -3 < 0; my $back_a_bit = $data[$i -3]; print chop($back_a_bit) eq '"' ? "$name: Found quote\n" : "$name +: No quote\n"; } }` [download] cheers tachyon s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print	[reply] [d/l]