probably stupid mistake

gogoglou has asked for the wisdom of the Perl Monks concerning the following question:

dear perl monks. I have the following piece of code which does something really trivial but I do not get any results. So what I want to do is first of all I have one array of keywords and one array of sentences. I want to print the keyword and the sentence if somewhere in the sentence the keyword appears. It was working with one line in each file but as soon as I introduced a second sentence it stopped working. I think that I am doing something really stupidly wrong. Please be kind enough to help me out. Thanks in advance for any help

#!/usr/bin/perl

my $filename1 = $ARGV[0];
my $filename2 = $ARGV[1];


open(INPUT, $filename1);
open(INPUT2,$filename2);

my $line;
my @fields1;
my $fields1;
my $line2;
my @fields2;
my $fields2;
my $i=0;


my $line;

while ($line =<INPUT>){
chomp $line;
$i++;
push (@fields1, $line);
}

while ($line2 =<INPUT2>){
chomp $line2;
push (@fields2, $line2);
}

foreach $fields1(@fields1){
  foreach $fields2(@fields2){
# print "$fields1\n";
# print "$fields2\n";
    if ($fields2 =~ m/$fields1/){
    print "success\n";
      }
   }
}

# foreach $fields1(@fields1){
#     if ($line2 =~m/$fields1/){
#     print "$line2\n";
#     }
#   }
# }

# foreach $fields1(@fields1){
# print "$fields1\n";
# }
#
[download]

Comment on probably stupid mistake Download Code

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Re: probably stupid mistake by toolic (Bishop) on Apr 01, 2011 at 13:41 UTC
Since you didn't show us any of your input, we can not reproduce your problem very easily (if at all). Please add a few relevant lines of your input files. One likely issue is that you need to use quotemeta `if ( $fields2 =~ m/\Q$fields1/ ) {` [download] use strict and warnings autodie Basic debugging checklist	[reply] [d/l]
Re^2: probably stupid mistake by gogoglou (Beadle) on Apr 01, 2011 at 13:52 UTC
oh sorry, well the contents of the first file looks like this (its going to be larger, not that it should matter): `GRB2 AFF4 GGGB C7orf42` [download] and of the second file like these KEGG_PATHWAY hsa04722:Neurotrophin signaling pathway 33 0.147 +86271171251902 4,04E+09 GRB2, CAMK2G, NFKB1, MAPKAPK2, MAGED1, +KRAS, MAP3K3, MAP3K1, BCL2, RAC1, GAB1, RHOA, CAMK2D, SH2B3, NGFRAP1, + SHC1, MAP2K7, FRS2, PIK3R1, IRS2, RELA, YWHAB, YWHAE, TP73, NRAS, MA +PK1, CRKL, JUN, NTRK2, CALM3, MAPK9, SORT1, RAP1A 575 124 50 +85 2.353.506.311.360.440 6,83E+11 6,83E+11 0.004929324234 +03758 KEGG_PATHWAY hsa05200:Pathways in cancer 63 0.2822833587239 + 1,86E+10 FGF18, FGF5, PPARD, FGF9, NFKB1, FGF13, PTEN, CCNE2, AC +VR1B, MAX, CDKN2B, RHOA, RALB, RALA, FAS, TPR, CHUK, RELA, RXRA, LEF1 +, CDK6, RB1, STK4, DAPK1, JUP, MAPK1, CCDC6, CRKL, HIF1A, NCOA4, JUN, + VEGFA, MAPK9, TRAF1, WNT5A, APC2, XIAP, GRB2, IGF1R, KRAS, ITGAV, BC +L2, RAC1, RUNX1, PIK3R1, APC, CEBPA, COL4A4, FZD8, COL4A1, IL8, VHL, +CREBBP, TGFBR2, SMAD2, FZD5, STAT3, NRAS, RASSF5, CDKN1B, ITGA6, RASS +F1, JAK1 575 328 5085 16.985.949.098.621.400 0.0031423 +34832759053 0.0010485440045103767 0.02269450903600312 KEGG_PATHWAY hsa04310:Wnt signaling pathway 35 0.156824088179 +94445 4,76E+10 WNT5A, PPARD, APC2, PPP2R5A, CAMK2G, PPP2R5C, PP +P3R1, RAC1, NFAT5, PPP3CB, RHOA, CAMK2D, FRAT2, PRKACA, CHP, PLCB1, F +BXW11, APC, FZD8, VANGL1, NLK, VANGL2, CREBBP, LEF1, SMAD2, FZD5, SEN +P2, SFRP5, SFRP1, CCND2, CSNK1E, JUN, MAPK9, SIAH1, PPP2R5E 575 + 151 5085 20.498.128.419.234.000 0.008008272140318184 0.0 +02008108692225119 0.05796850410908494 [download]	[reply] [d/l] [select]
Re^3: probably stupid mistake by toolic (Bishop) on Apr 01, 2011 at 13:58 UTC
When I run your code using your 2 input files, I get the following output: `success success` [download] You need to describe in much more detail what problem you are having.	[reply] [d/l]
Re^4: probably stupid mistake by SriniK (Beadle) on Apr 01, 2011 at 14:14 UTC
Re^4: probably stupid mistake by gogoglou (Beadle) on Apr 01, 2011 at 14:03 UTC
Re^5: probably stupid mistake by gogoglou (Beadle) on Apr 01, 2011 at 14:07 UTC
Some notes below your chosen depth have not been shown here
Re: probably stupid mistake by Popcorn Dave (Abbot) on Apr 01, 2011 at 20:26 UTC
The other monks have given you great advice but you might also look in to using the graphical Perl debugger PTKDB Using that has solved numerous problems I've had since you can step through the code and watch what's happening with your variables and how they change. To disagree, one doesn't have to be disagreeable - Barry Goldwater	[reply]
Re: probably stupid mistake by GrandFather (Saint) on Apr 02, 2011 at 22:53 UTC
Try running the following sample code and see if it is close to what you want to achieve. #!/usr/bin/perl use strict; use warnings; my $file1 = <<FILE1; GRB2 AFF4 GGGB C7orf42 FILE1 my $file2 = <<FILE2; KEGG_PATHWAY hsa04722:Neurotrophin signaling pathway 33 0.147 +86271171251902 4,04E+09 GRB2, CAMK2G, NFKB1, MAPKAPK2, MAGED1, +KRAS, MAP3K3, MAP3K1, BCL2, RAC1, GAB1, RHOA, CAMK2D, SH2B3, NGFRAP1, + SHC1, MAP2K7, FRS2, PIK3R1, IRS2, RELA, YWHAB, YWHAE, TP73, NRAS, MA +PK1, CRKL, JUN, NTRK2, CALM3, MAPK9, SORT1, RAP1A 575 124 50 +85 2.353.506.311.360.440 6,83E+11 6,83E+11 0.004929324234 +03758 KEGG_PATHWAY hsa05200:Pathways in cancer 63 0.2822833587239 + 1,86E+10 FGF18, FGF5, PPARD, FGF9, NFKB1, FGF13, PTEN, CCNE2, AC +VR1B, MAX, CDKN2B, RHOA, RALB, RALA, FAS, TPR, CHUK, RELA, RXRA, LEF1 +, CDK6, RB1, STK4, DAPK1, JUP, MAPK1, CCDC6, CRKL, HIF1A, NCOA4, JUN, + VEGFA, MAPK9, TRAF1, WNT5A, APC2, XIAP, GRB2, IGF1R, KRAS, ITGAV, BC +L2, RAC1, RUNX1, PIK3R1, APC, CEBPA, COL4A4, FZD8, COL4A1, IL8, VHL, +CREBBP, TGFBR2, SMAD2, FZD5, STAT3, NRAS, RASSF5, CDKN1B, ITGA6, RASS +F1, JAK1 575 328 5085 16.985.949.098.621.400 0.0031423 +34832759053 0.0010485440045103767 0.02269450903600312 KEGG_PATHWAY hsa04310:Wnt signaling pathway 35 0.156824088179 +94445 4,76E+10 WNT5A, PPARD, APC2, PPP2R5A, CAMK2G, PPP2R5C, PP +P3R1, RAC1, NFAT5, PPP3CB, RHOA, CAMK2D, FRAT2, PRKACA, CHP, PLCB1, F +BXW11, APC, FZD8, VANGL1, NLK, VANGL2, CREBBP, LEF1, SMAD2, FZD5, SEN +P2, SFRP5, SFRP1, CCND2, CSNK1E, JUN, MAPK9, SIAH1, PPP2R5E 575 + 151 5085 20.498.128.419.234.000 0.008008272140318184 0.0 +02008108692225119 0.05796850410908494 FILE2 open my $in1, '<', \$file1; my @keyWords; while (defined (my $line = <$in1>)) { chomp $line; push @keyWords, $line; } close $in1; die "No keywords specified\n" if ! @keyWords; my $match = "\\b\Q" . join ("\E\\b\|\b\Q", @keyWords) . "\E\\b"; open my $in2, '<', \$file2; while (defined (my $line = <$in2>)) { next if $line !~ /($match)/; print "Matched $1 in line $.\n"; } [download] Prints: `Matched GRB2 in line 1 Matched GRB2 in line 2` [download] Some stuff to notice: Use inline data for sample or test code so you don't have to deal with external files. Use three parameter open and lexical file handles. Don't slurp files into an array then loop over the array. Avoid nested loops. Keep variable declarations local to where they are used. Always use strictures (use strict; use warnings;). Use meaningful variable names Remove unused code and variables ($i was not used and was redundant in any case). True laziness is hard work	[reply] [d/l] [select]