Reading an entire file into a hash in Perl

Question

I have some problems reading a file into a hash in Perl.

Chr1_supercontig_000000000  1   500
    PILOT21_588_1_3_14602_59349_1
Chr1_supercontig_000000001  5   100
    PILOT21_588_1_21_7318_90709_1
    PILOT21_588_1_43_18803_144592_1
    PILOT21_588_1_67_13829_193943_1
    PILOT21_588_1_42_19678_132419_1
    PILOT21_588_1_67_4757_125247_1
...

So I have this file above. My desired output is a hash with the "Chr1"-lines as key, and the "PILOT"-lines as values.

Chr1_supercontig_000000000 => PILOT21_588_1_3_14602_59349_1
Chr1_supercontig_000000001 => PILOT21_588_1_21_7318_90709_1, PILOT21_588_1_43_18803_144592_1,...

As far as I know, multiple values can be assigned to a key only by reference, is that correct?

I got stuck at this point and need help.

Answer 1

You can read the file line-by-line keeping track of the current hash key:

open my $fh, '<', 'file' or die $!;

my (%hash, $current_key);

while (<$fh>) {
    chomp;        
    $current_key = $1, next if /^(\S+)/;
    s/^\s+//; # remove leading space
    push @{ $hash{$current_key} }, $_;
}

Answer 2

Here is another fairly short, clear version:

while (<>) {
   if(/^Chr\S+/) {
      $c=$&;
   } else {
      /\S+/;
      push @{ $p{$c} }, $&;
   }
}

And to print the results:

foreach my $pc ( sort keys %p ) {
   print "$pc => ".join(", ", @{$p{$pc}})."\n";
}

This is a shorter print-results (but the first one seems more readable to me):

map { print "$_ => ".join(", ", @{$p{$_}})."\n" } sort keys %p;

One-liner from command line:

perl <1 -e 'while(<>){ if(/^Chr\S+/){ $c=$&; }else{ /\S+/; push(@{$p{$c}},$&);} } map { print "$_ => ".join(", ", @{$p{$_}})."\n" } sort keys %p;'

Answer 3

Try this ,

#!/usr/bin/perl 
use strict;
use warnings;
use Data::Dumper;

my ( $fh,$cur );
my $hash = ();
open $fh,'<' , 'file' or die "Can not open file\n";

while (<$fh> ) {
    chomp;
    if ( /^(Chr.+? ).+/ ) {
        $cur = $1;
        $hash->{$cur} = '';
    }
    else {
        $hash->{$cur} = $hash->{$cur} .$_ . ',';
    }
}

print Dumper $hash;

Answer 4

Many good answers already, so I'll add one that does not rely on regexes, but rather on that the key-lines contain three space/tab delimited entries, and the values only one.

It will automatically strip leading whitespace and newlines, and so is somewhat convenient.

use strict;
use warnings;

my %hash;
my $key;

while (<DATA>) {
    my @row = split;
    if (@row > 1) {
        $key = shift @row;
    } else {
        push @{$hash{$key}}, shift @row;
    }
}

use Data::Dumper;
print Dumper \%hash;

__DATA__
Chr1_supercontig_000000000  1   500
    PILOT21_588_1_3_14602_59349_1
Chr1_supercontig_000000001  5   100
    PILOT21_588_1_21_7318_90709_1
    PILOT21_588_1_43_18803_144592_1
    PILOT21_588_1_67_13829_193943_1
    PILOT21_588_1_42_19678_132419_1
    PILOT21_588_1_67_4757_125247_1

Answer 5

How about:

#!/usr/bin/perl 
use strict;
use warnings;
use Data::Dump qw(dump);

my %hash;
my $key;
while(<DATA>) {
    chomp;
    if (/^(Chr1_supercontig_\d+)/) {
        $key = $1;
        $hash{$key} = ();
    } else {
        push @{$hash{$key}}, $_;
    }
}
dump%hash;

__DATA__
Chr1_supercontig_000000000  1   500
    PILOT21_588_1_3_14602_59349_1
Chr1_supercontig_000000001  5   100
    PILOT21_588_1_21_7318_90709_1
    PILOT21_588_1_43_18803_144592_1
    PILOT21_588_1_67_13829_193943_1
    PILOT21_588_1_42_19678_132419_1
    PILOT21_588_1_67_4757_125247_1

output:

(
  "Chr1_supercontig_000000001",
  [
    "    PILOT21_588_1_21_7318_90709_1",
    "    PILOT21_588_1_43_18803_144592_1",
    "    PILOT21_588_1_67_13829_193943_1",
    "    PILOT21_588_1_42_19678_132419_1",
    "    PILOT21_588_1_67_4757_125247_1",
  ],
  "Chr1_supercontig_000000000",
  ["    PILOT21_588_1_3_14602_59349_1"],
)

Answer 6

You are right, the hash values need to be references that point to arrays which contain the PILOT lines.

Here's a way to do it:

my %hash;
open FILE, "filename.txt" or die $!;
my $key;
while (my $line = <FILE>) {
     chomp($line);
     if ($line !~ /^\s/) {
        ($key) = $line =~ /^\S+/g;
        $hash{$key} = [];
     } else {
        $line =~ s/^\s+//;
        push @{ $hash{$key} }, $line;
     }
 }
 close FILE;