写一个perl代码通过基因组文件提取最长转录本
时间: 2023-06-03 17:07:54 浏览: 69
以下是Perl代码实现:
#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
# 输入基因组文件
my $fasta = Bio::SeqIO->new(-file => "genome.fa", -format => 'fasta');
# 输入转录本信息文件
open(my $fh, "<", "transcripts.txt") or die "Can't open transcripts file: $!\n";
my %transcripts;
while (my $line = <$fh>) {
chomp($line);
my ($transcript_id, $gene_id, $start, $stop) = split("\t", $line);
push @{$transcripts{$gene_id}}, [$transcript_id, $start, $stop];
}
close($fh);
# 记录最长转录本信息
my %longest_transcripts;
while (my $seq = $fasta->next_seq()) {
my $gene_id = $seq->id();
if (exists $transcripts{$gene_id}) {
my $longest_length = 0;
my $longest_transcript_id;
foreach my $transcript (@{$transcripts{$gene_id}}) {
my ($transcript_id, $start, $stop) = @{$transcript};
my $length = $stop - $start + 1;
if ($length > $longest_length) {
$longest_length = $length;
$longest_transcript_id = $transcript_id;
}
}
$longest_transcripts{$gene_id} = $longest_transcript_id;
}
}
# 输出最长转录本序列
foreach my $gene_id (sort keys %longest_transcripts) {
my $seq = $fasta->seq($gene_id);
my $longest_transcript_id = $longest_transcripts{$gene_id};
if (defined $longest_transcript_id) {
print ">$longest_transcript_id\n";
my ($start, $stop) = @{$transcripts{$gene_id}[0]}[1,2];
my $longest_seq = substr($seq, $start-1, $stop-$start+1);
print "$longest_seq\n";
}
}