按唯一值和最大值过滤文件;将两个数组合并为哈希

Question

我需要在一列中按唯一属(物种名称的第一部分(提取，但在 CSV 文件中具有多个相同名称时，需要在另一列中按最大数字提取。

因此，如果有多个属(相同的名字(，则在最后一列中取最大的数字来选择哪个将代表该属。

我已经将信息提取到数组中，但是在将两者结合起来进行选择时遇到了问题。 我正在使用https://perlmaven.com/unique-values-in-an-array-in-perl为了提供帮助，但是当具有相同的属情况时，我需要在最后一列中包含最大的数字。

use strict;
use warnings;
open taxa_fh, '<', "$ARGV[0]" or die qq{Failed to open "$ARGV[0]" for input: $!n};
open match_fh, ">$ARGV[0]_genusLongestLEN.csv" or die qq{Failed to open for output: $!n};my @unique;
my %seen;
my %hash;
while ( my $line = <taxa_fh> ) {
   chomp( $line );
   my @parts = split( /,/, $line );
   my @name = split( / /, $parts[3]);
   my @A = $name[0];
   my @B = $parts[5];
   @seen{@A} = ();
   my @merged = (@A, grep{!exists $seen{$_}} @B);
   my @merged = (@A, @B);
   @hash{@A} = @B;
   print "$linen";
}
close taxa_fh;
close match_fh;

输入示例：

AB179735.1.1711,AB179735.1.1711,278983,Eucyrtidium hexagonatum,0,1600
AB179736.1.1725,AB179736.1.1725,278986,Pterocorys zancleus,0,1763
AB181888.1.1758,AB181888.1.1758,281609,Protoperidinium crassipes,0,1700
AB181890.1.1709,AB181890.1.1709,281610,Protoperidinium denticulatum,0,1800
AB181892.1.1738,AB181892.1.1738,281611,Protoperidinium divergens,0,1800
AB181894.1.1744,AB181894.1.1744,281612,Protoperidinium leonis,0,1500
AB181899.1.1746,AB181899.1.1746,281613,Protoperidinium pallidum,0,1600
AB181902.1.1741,AB181902.1.1741,261845,Protoperidinium pellucidum,0,1750
AB181904.1.1734,AB181904.1.1734,281614,Protoperidinium punctulatum,0,1599
AB181907.1.1687,AB181907.1.1687,281615,Protoperidinium thorianum,0,1600
AB120001.1.1725,AB120001.1.1725,244960,Gyrodinium spirale,0,1500
AB120002.1.1725,AB120002.1.1725,244961,Gyrodinium fusiforme,0,1800
AB120003.1.1724,AB120003.1.1724,244962,Gyrodinium rubrum,0,1700
AB120004.1.1723,AB120004.1.1723,244963,Gyrodinium helveticum,0,1500
AB120309.1.1800,AB120309.1.1800,4442,Camellia sinensis,0,1700

想要的输出：

AB179735.1.1711,AB179735.1.1711,278983,Eucyrtidium hexagonatum,0,1600
AB179736.1.1725,AB179736.1.1725,278986,Pterocorys zancleus,0,1763
AB181890.1.1709,AB181890.1.1709,281610,Protoperidinium denticulatum,0,1800
AB120002.1.1725,AB120002.1.1725,244961,Gyrodinium fusiforme,0,1800
AB120309.1.1800,AB120309.1.1800,4442,Camellia sinensis,0,1700

Answer 1

use Text::CSV_XS qw( );
my $csv = Text::CSV_XS->new({
   auto_diag   => 2,
   binary      => 1,
   quote_space => 0,
});
my %by_genus;
while ( my $row = $csv->getline(*ARGV) ) {
   my ($genus) = split(' ', $row->[3]);
   $by_genus{$genus} = $row
      if !$by_genus{$genus}
      || $row->[5] > $by_genus{$genus}[5];
}
$csv->say(select(), $_) for values(%by_genus);

Answer 2

正确命名变量可使代码更具可读性：

#! /usr/bin/perl
use warnings;
use strict;
my %selected;
while (<>) {
    my ($species, $value) = (split /,/)[3, 5];
    my $genus = (split ' ', $species)[0];
    if ($value > ($selected{$genus}{max} || 0)) {
        $selected{$genus}{max} = $value;
        $selected{$genus}{line} = $_;
    }
}
for my $genus (keys %selected) {
    print $selected{$genus}{line};
}

输出行的顺序是随机的。

Answer 3

你也可以使用Perl命令行

perl -F, -lane ' ($g=$F[3])=~s/(^S+).*/$1/; if( $mx{$g}<$F[-1]) 
   { $kv{$g}=$_;$mx{$g}=$F[-1] } END { print $kv{$_} for(keys %kv) } ' file

在 cara.txt 文件中给定输入时，输出为

$ perl -F, -lane ' ($g=$F[3])=~s/(^S+).*/$1/; if( $mx{$g}<$F[-1]) 
       { $kv{$g}=$_;$mx{$g}=$F[-1] } END { print $kv{$_} for(keys %kv) }  ' cara.txt
AB179736.1.1725,AB179736.1.1725,278986,Pterocorys zancleus,0,1763
AB179735.1.1711,AB179735.1.1711,278983,Eucyrtidium hexagonatum,0,1600
AB120309.1.1800,AB120309.1.1800,4442,Camellia sinensis,0,1700
AB120002.1.1725,AB120002.1.1725,244961,Gyrodinium fusiforme,0,1800
AB181890.1.1709,AB181890.1.1709,281610,Protoperidinium denticulatum,0,1800
$

Answer 4

不花哨，但可以完成工作

#!/usr/bin/perl
use strict;
my @data = `cat /var/tmp/test.in`;
my %genuses = ();

foreach my $line ( @data ) {
  chomp($line);
  my @splitline = split(',', $line);
  my $genus = $splitline[3];
  my $num = $splitline[5];
  my ( $name, $extra ) = split(' ', $genus);
  if ( exists $genuses{$name}->{'num'} ) {
    if ( $genuses{$name}->{'num'} < $num ) {
      $genuses{$name}->{'num'} = $num;
      $genuses{$name}->{'line'} = $line;
    }
    else {
        next;
    }
  }
  else {
    $genuses{$name}->{'num'} = $num;
    $genuses{$name}->{'line'} = $line;
 }
}
foreach my $genus ( %genuses ) {
  print "$genuses{$genus}->{'line'}";
  print "n";
}

输出：

[root@localhost tmp]# ./test.pl
AB179736.1.1725,AB179736.1.1725,278986,Pterocorys zancleus,0,1763
AB179735.1.1711,AB179735.1.1711,278983,Eucyrtidium hexagonatum,0,1600
AB120309.1.1800,AB120309.1.1800,4442,Camellia sinensis,0,1700
AB120002.1.1725,AB120002.1.1725,244961,Gyrodinium fusiforme,0,1800
AB181890.1.1709,AB181890.1.1709,281610,Protoperidinium denticulatum,0,1800

没有看到您按输出进行排序的明显方法