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问题:
I have a file which looks like this:
80,1p21 81,19q13 82,6p12.3 83,Xp11.22 84,3pter-q21 86,3q26.33 87,14q24.1-q24.2|14q24|14q22-q24 88,1q42-q43 89,11q13.1 90,2q23-q24 91,12q13 92,2q22.3 93,3p22 94,12q11-q14 95,3p21.1 97,14q24.3 98,2p16.2
And I want to sort them based on second column. And the first column should change accordingly too. When you use sort command in perl, it doesn't do it because it says its not numeric. Is there a way to sort things alpha numerically in perl?
Thanks.
回答1:
If you read the documentation for sort, you'll see that you don't need to do a numeric sort in Perl. You can do string comparisons too.
@sorted = sort { $a cmp $b } @unsorted;
But that still leaves you with a problem as, for example, 19q will sort before 6p. So you can write your own sort function which can make whatever transformations you want before doing the comparison.
@sorted = sort my_complex_sort @unsorted; sub my_complex_sort { # code that compares $a and $b and returns -1, 0 or 1 as appropriate # It's probably best in most cases to do the actual comparison using cmp or <=> # Extract the digits following the first comma my ($number_a) = $a =~ /,(\d+)/; my ($number_b) = $b =~ /,(\d+)/; # Extract the letter following those digits my ($letter_a) = $a =~ /,\d+(a-z)/; my ($letter_b) = $b =~ /,\d+(a-z)/; # Compare and return return $number_a <=> $number_b or $letter_a cmp $letter_b; }
回答2:
#!/usr/bin/env perl use strict; use warnings; my @datas = map { /^(\d+),(\d*)(.*)$/; [$1, $2, $3]; } <DATA>; my @res = sort {$a->[1] <=> $b->[1] or $a->[2] cmp $b->[2]} @datas; foreach my $data (@res) { my ($x, $y, $z) = @{$data}; print "$x,$y$z\n"; } __DATA__ 80,1p21 81,19q13 82,6p12.3 83,Xp11.22 84,3pter-q21 86,3q26.33 87,14q24.1-q24.2|14q24|14q22-q24 88,1q42-q43 89,11q13.1 90,2q23-q24 91,12q13 92,2q22.3 93,3p22 94,12q11-q14 95,3p21.1 97,14q24.3 98,2p16.2
回答3:
I actually found the answer to this. The code looks a bit complicated though.
#!/usr/bin/env perl use strict; use warnings; sub main { my $file; if (@ARGV != 1) { die "Usage: perl hashofhash_sort.pl <filename>\n"; } else { $file = $ARGV[0]; } open(IN, $file) or die "Error!! Cannot open the $file file: $!\n"; my @file = <IN>; chomp @file; my ($entrez_gene, $loci, $chr, $band, $pq, $band_num); my (%chromosome, %loci_entrez); foreach my $line (@file) { if ($line =~ /(\d+),(.+)/) { # Entrez genes $entrez_gene = $1; # Locus like 12p23.4 $loci = $2; if ($loci =~ /^(\d+)(.+)?/) { # chromosome number alone (only numericals) $chr = $1; if ($2) { # locus minus chromosome number. If 12p23.4, then $band is p23.4 $band = "$2"; if ($band =~ /^([pq])(.+)/) { # either p or q $pq = $1; # stores the numericals. for p23.4, stores 23.4 $band_num = $2; } if (exists $chromosome{$chr}) { if (exists $chromosome{$chr}{$pq}) { push (@{$chromosome{$chr}{$pq}}, $band_num); } else { $chromosome{$chr}{$pq} = [$band_num]; } } else { $chromosome{$chr}{$pq} = [$band_num]; } } } } } # End of foreach loop foreach my $key (sort {$a <=> $b} keys %chromosome) { my %seen = (); foreach my $key2 (sort {$a cmp $b } keys %{$chromosome{$key}}) { my @unique = grep { ! $seen{$_}++ } @{$chromosome{$key}{$key2}}; my @sorted = sort @unique; foreach my $element (@sorted) { my $sorted_locus = "$key$key2$element"; if (exists $loci_entrez{$sorted_locus}) { foreach my $element2 (@{$loci_entrez{$sorted_locus}}) { print "$element2,$sorted_locus\n"; } } } } } } # End of main main();
