Perl去重fasta序列

2024-09-01 20:41:51

常规方法

#! usr/bin/perl -w

use strict;

my $input=shift;

my %hash;

open IN,"<$input";

$/=">";

while(<IN>){

    chomp;

    $hash{$_}=1;

}

foreach my $key(keys %hash){

    print ">$key";

}

close IN;

Bioseq模块方法

#！/usr/bin/perl

use Bio::SeqIO;

my $fas=shift @ARGV;

my $IN=Bio::SeqIO->new(-file=>"$fas",-format=>'fasta');

my $OUT=Bio::SeqIO->new(-file=>">New_$fas",-format=>'fasta');

my $check={};

while (my $seq=$IN->next_seq()){

    my $id=$seq->id;

    unless($check->{$id}){

       $check->{$id}=1;

       $OUT->write_seq($seq);

    }

}

$IN->close();

$OUT->close();

print "Finished!\n";

单行命令

cat cat_allsample.fa |perl -076 -ne 'chomp; print ">$_" unless $c{$_}++ '|grep -c '>'

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