CODEWITHSUNDEEP
perlunixsplittruncate
Gaia Andreoletti
Gaia Andreoletti

Reputation: 51

Split a file in several output

I am trying to divide a big file into different files containing single information for each variable inside the file.

my input file look like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  PID008SM

...info here 1.....

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CL001-SC

....info here 2....

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CL001-SC

....info here 3....        

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  PID008SM

....info here 4....

In this case I would like to create two output file (one for PID008SM and CL001-SC) with the information related to each of them.

Output for CL001-SC:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CL001-SC

....info here 2...

....info here 3...

Output for PID008SM

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  PID008SM
....info here 1....

....info here 4....

The script that I have used is in Perl but any suggestion it is more than welcome. Thank you in advance.

code:

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

my $file1 = $ARGV[0] ;
my $file2 = $ARGV[1];

open (F1, $file1); #Opens first .vcf file for comparison
open (F2, $file2); #2nd for comparison

my %file;

## Create the hash key with each line of the file2
while (<F2> ) {
        #chomp;
        $file{$_}='';
}

## Print the line , if key   exist in the hash ;       

foreach my $string (<F1>) {

        if ( exists $file{$_}) and ($string =~ /(#)(.+?)(#)/s) {
                print $string;
        }
}

Upvotes: 0

Views: 148

Answers (2)

Borodin
Borodin

Reputation: 126742

Something like this perhaps?

use strict;
use warnings;

open my $fh, '<', 'chrom.txt' or die $!;

my %fh;

while (<$fh>) {

  if ( /^#CHROM/ ) {

    my $name =  (split)[-1];

    if ($fh{$name}) {
      select $fh{$name};
      next;
    }

    my $file = "$name.txt";
    open $fh{$name}, '>', $file or die qq{Unable to open "$file" for output: $!};
    print STDOUT qq{Created file "$file"\n};
    select $fh{$name};
  }

  print;
}

Upvotes: 1

Sidharth C. Nadhan
Sidharth C. Nadhan

Reputation: 2253

awk '/^#CHROM/{typ=$10;a[$0]++} a[$0]<2{print >> typ}' inputFile

this awk script seems to work +

Upvotes: 0

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