Re^4: match pattern from two different file

[vinoth.ree]

Ok, then just remove the following if condition from my code and print the $line1

#!/usr/bin/perl
use strict;
use warnings;

open(FH, "<","./file1.txt") or die "Can't Open File1\n";
open(BH, "<","./file2.txt") or die "Can't Open File2\n";

my $pattern='^LOC_Os0[1-7]g[0-9]*.[0-9]\s';

while(my $line1 = <FH>)
{
        chomp($line1);
        #print "Line1:$line1\n";
        if( $line1=~ /$pattern/)
        {
                while(my $line2 = <BH>)
                {
                        chomp($line2);

                        if($line2 =~ /$pattern/)
                        {                                  
                            print "Matches: ". $line1;
                        }
                        else
                        {
                            print "nothing to print\n";
                        }
                        
                }
                seek(BH,0,0);
        }
}
close(FH);
close(BH);

[Anonymous Monk]

Thank u very very much, u r life saver (maybe I am exaggerating), but I am really thankful for your help.
God Bless You

[Anonymous Monk]

hi vinoth.ree
hello again
can u help once again
I was using code u hv written and it was working fine. but earlier my file has redundancy so output, as u can imagine from pattern matching, was huge.
so before pattern match i thought to remove redundancy from both the input files.
but non redundant input file for pattern matching is not giving output as it should (resulting output file have multiple entries making file redundant ad bulky again). my files


file 1
LOC_Os01g01010.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01010.2 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01019.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01030.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01040.4 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01040.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01040.3 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01040.2 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01050.2 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01050.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01060.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01070.3 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01070.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01070.2 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01080.2 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01080.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01080.3 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01090.1 : PS00022 EGF_1 EGF-like domain signature 1.
LOC_Os01g01100.1 : PS00022 EGF_1 EGF-like domain signature 1.

file 2

LOC_Os01g01010.1 3017 : uORF [3,233] : ATG AGCTGGTGGGGATGCTCTAAGAGAACG
+AGAGAAGCACAGAGCAGATAAACCACACCCACAGGCACCACCGTCCTTGTTGGTAATGAAGAAGACGAG
+ACGACGACTTCCCCACTAGGAAACACGACGGAGGCGGAGATGATCGACGGCGGAGAGAGCTACAGAAAC
+ATCGATGCCTCCTGTCCAATCCCCCCATCCCATTCGGTAGTTGGATTGAAGACTACCGAA TAA
LOC_Os01g01010.2 2218 : uORF [7,129] : ATG AAGAAGACGAGACGACGACTTCCCCAC
+TAGGAAACACGACGGAGGCGGAGATGATCGACGGCGGAGAGAGCTACAGAAACATCGATGCCTCCTGTC
+CAATCCCCCCATCCCATTCGG TAG
LOC_Os01g01019.1 1127 : CPE [1010,1127] : TTTTTAAT TTTTCGATAGCCAAATATT
+AACTATTTAGCGACTTTATTGTCTGGTGTCCGAAGAAGAATATATGTAAATGACATTACCAT AATAAA
+ TGTTGAATGCTTCATCAAATTTT 
LOC_Os01g01030.1 2464 : IRES [2366,2464] : TAACT GAATTA GTATTC TA AGAA
+T ATGTC AGTTT ACAAT CTTA ATTCT TAA GAAAGT CTAAA AGTCG TGC ATGTGC GTTC
+CGA GCACAC ACTTTTTCGT 
LOC_Os01g01040.4 1524 : IRES [1436,1524] : AACTA CATT GTGGAG AT TAGCAA
+ CGAAAAT GTGCTA GGCCC AGGT GAGCT T TTCTAG  TGATT GT TGATA CCTACATA AG
+TCA TCTTTCC 
LOC_Os01g01040.1 2508 : IRES [2418,2508] : TGTTG TTGTT GACTA T GTGGT A
+CTTTGT GATGC TTGGA CATG TTTAT ATG TGGTG CTATGT TAAAA AATCC TGTTG AAA 
+TTGTG TCAATTA 
LOC_Os01g01040.3 2583 : IRES [2493,2583] : TGTTG TTGTT GACTA T GTGGT A
+CTTTGT GATGC TTGGA CATG TTTAT ATG TGGTG CTATGT TAAAA AATCC TGTTG AAA 
+TTGTG TCAATTA 
LOC_Os01g01040.2 2482 : IRES [2392,2482] : TGTTG TTGTT GACTA T GTGGT A
+CTTTGT GATGC TTGGA CATG TTTAT ATG TGGTG CTATGT TAAAA AATCC TGTTG AAA 
+TTGTG TCAATTA 
LOC_Os01g01050.2 1996 : IRES [1911,1996] : GTTGG TCTCA TTTTCG TT TGCTG
+ CTGGTTAC TTGTA TTAAT ACATT ATAGA AAA TGAGTA CA TAAAT AT ACATG ACGA T
+ATGA TCC 
LOC_Os01g01050.1 2039 : IRES [1954,2039] : GTTGG TCTCA TTTTCG TT TGCTG
+ CTGGTTAC TTGTA TTAAT ACATT ATAGA AAA TGAGTA CA TAAAT AT ACATG ACGA T
+ATGA TCC 
LOC_Os01g01060.1 920 : K-BOX [778,785] : CTGTGATT
LOC_Os01g01070.3 1369 : uORF [19,87] : ATG CGAACGAGCACCGGATCCGCTGCGGCT
+GCTCGGCGTCGGGTCGGAGGTGAGGTCTCGAAACCC TAG
LOC_Os01g01070.1 1568 : IRES [1465,1568] : AGCAAG TTTGTT TGGGG AG GATG
+TACT GGAATAAG GGTATAGT AGTAGTA GGAAT TATTATG GCAC ATTTG  CATGCT TT GG
+CATA TGGCACTC TGAGTT TTATT 
LOC_Os01g01070.2 1562 : IRES [1459,1562] : AGCAAG TTTGTT TGGGG AG GATG
+TACT GGAATAAG GGTATAGT AGTAGTA GGAAT TATTATG GCAC ATTTG  CATGCT TT GG
+CATA 


I only want to match the pattern 
 "(LOC_Os0[1-7]g[0-9]*.[0-9])\s"

[poj]

Use a hash if you want to ignore the duplicates, like this

#!/usr/local/bin/perl
use strict;
use warnings;

my $pattern = qr'^LOC_Os0[1-7]g[0-9]*.[0-9]\s';

# read files
my $hash1 = parse_file('file1.txt');
my $hash2 = parse_file('file2.txt');

# report
my $count=0;
for my $loc (sort keys %$hash1){
  if ( exists $hash2->{$loc} ){
    print "$loc\n";
    ++$count;
  }
}
print "$count unique patterns in both files\n";

# parse file
sub parse_file{
  my $filename = shift;
  my %hash=(); my $count=0;
  open FH,'<',$filename or die "Can't Open $filename\n";
  while ( my $line = <FH> ){
    if ( $line =~ /($pattern)/ ){
      $hash{$1} = 1;
    }  
    ++$count;
  }
  close FH;
  print "$count lines read from $filename\n";
  return \%hash;
}

poj