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

Salutations , O Great and Wise Monks . I as a total apprentice seek your wisdom and knowledge. On the following problem : I have two files (xname1 xname2 ) the information in those files is structured like this xname1 :

 
FBgn0041711    yellow-e    FBgn0038150
FBgn0041711    yellow-e    FBgn0039896
FBgn0041711    yellow-e    FBgn0032601
FBgn0041711    yellow-e    FBgn0038151
FBgn0041711    yellow-e    FBgn0041713
FBgn0041711    yellow-e    FBgn0041710
FBgn0041711    yellow-e    FBgn0041712
FBgn0041711    yellow-e    FBgn0034856
FBgn0041711    yellow-e    FBgn0038105
FBgn0041711    yellow-e    FBgn0041709
FBgn0041711    yellow-e    FBgn0035328
FBgn0041711    yellow-e    FBgn0004034
FBgn0032283    CG7296    
FBgn0042110    CG18765    FBgn0039328
FBgn0042110    CG18765    FBgn0039325

[download]

the information in the other file is structured in the same way xname2 :

 
FBgn0041711|FBtr0082757    F    dme-miR-iab-4-5p MIMAT0000412    25   
+ seven_m8
FBgn0041711|FBtr0082757    F    dme-miR-2280-3p MIMAT0011787    51    
+seven_A1
FBgn0041711|FBtr0082757    F    dme-miR-955-3p MIMAT0020847    69    e
+ightmer
FBgn0041711|FBtr0082757    F    dme-miR-4957-3p MIMAT0020176    43    
+seven_A1 
FBgn0039896|FBtr0089115    F    dme-miR-2280-3p MIMAT0011787    9    s
+even_A1
FBgn0039896|FBtr0089115    F    dme-miR-4943-5p MIMAT0020151    12    
+seven_m8 
FBgn0041711|FBtr0082757    F    dme-miR-2280-3p MIMAT0011787    51    
+seven_A1 *
FBgn0039328|FBtr0084849    F    dme-miR-977-3p MIMAT0005493    92    s
+even_A1
FBgn0039328|FBtr0084849    F    dme-miR-967-5p MIMAT0005482    92    s
+even_A1
FBgn0039328|FBtr0084849    F    dme-miR-4943-5p MIMAT0020151    143   
+ seven_m8
FBgn0039328|FBtr0084849    F    dme-miR-4967-5p MIMAT0020192    99    
+seven_m8
FBgn0039290|FBtr0084805    F    dme-miR-2501-5p MIMAT0012216    583   
+ eightmer

[download]

So what I strive to achieve is the following thing . I need a loop that goes trough every line in the first and second documents (array list) and if it finds a matching Fbgn from the first document to the second document (be it the firs one or the second one FBgn in a line) to paste the dme-mir only or the whole line below (preferably the dme-mir only) the found match. It should look something like this : 

 
FBgn0041711    yellow-e    FBgn0038150
FBgn0041711|FBtr0082757    F    dme-miR-iab-4-5p MIMAT0000412    25   
+ seven_m8
FBgn0041711|FBtr0082757    F    dme-miR-2280-3p MIMAT0011787    51    
+seven_A1
FBgn0041711|FBtr0082757    F    dme-miR-955-3p MIMAT0020847    69    e
+ightmer
FBgn0041711|FBtr0082757    F    dme-miR-4957-3p MIMAT0020176    43    
+seven_A1
FBgn0041711|FBtr0082757    F    dme-miR-2280-3p MIMAT0011787    51    
+seven_A1 *
FBgn0041711    yellow-e    FBgn0039896
FBgn0039896|FBtr0089115    F    dme-miR-2280-3p MIMAT0011787    9    s
+even_A1
FBgn0042110    CG18765    FBgn0039328
FBgn0039328|FBtr0084849    F    dme-miR-967-5p MIMAT0005482    92    s
+even_A1
FBgn0039328|FBtr0084849    F    dme-miR-4943-5p MIMAT0020151    143   
+ seven_m8
                                                        dme-miR-4943-5
+p

[download]

The last line is the other variant with the dme-mir only . I'm really sorry if I didn't make it clear and for my noobish question. All help will be greatly appreciated! Thanks again and have a nice day.

Replies are listed 'Best First'.
Re: Duplicates in arrays and add values
by poj (Abbot) on Mar 09, 2016 at 16:01 UTC

    Try

    #!perl 
use strict;

my $file2 = 'xname2.txt';
open IN,'<',$file2 or die "Could not open $file2 : $!";
my %file2 = (); 
while (<IN>){
  next unless /\S/;
  my ($FBgn) = split '\|';
  push @{$file2{$FBgn}},$_;
}

my $file1 = 'xname1.txt';
open IN,'<',$file1 or die "Could not open $file1 : $!";
while (my $line = <IN>){
  next unless $line =~ /\S/;
  for (split /\s+/,$line){
    next unless /^FBgn/;
    if (exists $file2{$_}){
      print join '',$line,@{$file2{$_}};
      delete $file2{$_};
    }
  }
}

    [download]
    poj
[reply]
[d/l]

      Thank you both of you. I really appreciate what both of you did. Poj man if you are in Manchester give me your address I'm going to deliver you couple of beers or what ever you want. Thank you masters again . Have a nice evening.

[reply]
Re: Duplicates in arrays and add values
by 1nickt (Canon) on Mar 09, 2016 at 15:34 UTC

    Hi Waterdrake, you'll get better help if you show what you've tried, and how it fails for you.

    Also, if you search this site using the Super Search, you'll find that this is a common problem that has been asked about before, and you'll probably find your answers.

    Post back here when you get stuck, after you've tried some things. Good luck!

    The way forward always starts with a minimal test.
[reply]
[d/l]

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