用Perl编写代码从注释文件（sequence.fasta。annotation.gff）中提取CDS序列并翻译序列

使用Perl编写代码从注释文件（sequence.fasta和annotation.gff）中提取CDS序列并翻译序列，可以按照以下步骤进行： 1. 读取FASTA文件并存储序列。 2. 读取GFF文件并提取CDS区域。 3. 根据CDS区域从FASTA序列中提取相应的序列。 4. 将提取的CDS序列翻译成蛋白质序列。 下面是一个示例代码： ```perl use strict; use warnings; use Bio::SeqIO; # 读取FASTA文件并存储序列 my $fasta_file = 'sequence.fasta'; my $seqio = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); my %sequences; while (my $seq = $seqio->next_seq) { $sequences{$seq->id} = $seq->seq; } # 读取GFF文件并提取CDS区域 my $gff_file = 'annotation.gff'; open(my $fh, '<', $gff_file) or die "Cannot open $gff_file: $!"; my %cds_regions; while (my $line = <$fh>) { next if $line =~ /^#/; chomp $line; my @fields = split(/\t/, $line); my ($seq_id, $source, $feature, $start, $end, $score, $strand, $frame, $attribute) = @fields; if ($feature eq 'CDS') { push @{$cds_regions{$seq_id}}, { start => $start, end => $end, strand => $strand }; } } close($fh); # 提取CDS序列并翻译 foreach my $seq_id (keys %cds_regions) { my $sequence = $sequences{$seq_id}; foreach my $cds (@{$cds_regions{$seq_id}}) { my $cds_seq = substr($sequence, $cds->{start} - 1, $cds->{end} - $cds->{start} + 1); $cds_seq = reverse_complement($cds_seq) if $cds-'; my $protein_seq = translate($cds_seq); print ">$seq_id:$cds->{start}-$cds->{end}:$cds->{strand}\n$protein_seq\n"; } } # 反向互补序列 sub reverse_complement { my ($seq) = @_; $seq = reverse $seq; $seq =~ tr/ACGTacgt/TGCAtgca/; return $seq; } # 翻译序列 sub translate { my ($seq) = @_; my %codon_table = ( 'TCA' => 'S', 'TCC' => 'S', 'TCG' => 'S', 'TCT' => 'S', 'TTC' => 'F', 'TTT' => 'F', 'TTA' => 'L', 'TTG' => 'L', 'TAC' => 'Y', 'TAT' => 'Y', 'TAA' => '*', 'TAG' => '*', 'TGC' => 'C', 'TGT' => 'C', 'TGA' => '*', 'TGG' => 'W', 'CTA' => 'L', 'CTC' => 'L', 'CTG' => 'L', 'CTT' => 'L', 'CCA' => 'P', 'CCC' => 'P', 'CCG' => 'P', 'CCT' => 'P', 'CAC' => 'H', 'CAT' => 'H', 'CAA' => 'Q', 'CAG' => 'Q', 'CGA' => 'R', 'CGC' => 'R', 'CGG' => 'R', 'CGT' => 'R', 'ATA' => 'I', 'ATC' => 'I', 'ATT' => 'I', 'ATG' => 'M', 'ACA' => 'T', 'ACC' => 'T', 'ACG' => 'T', 'ACT' => 'T', 'AAC' => 'N', 'AAT' => 'N', 'AAA' => 'K', 'AAG' => 'K', 'AGC' => 'S', 'AGT' => 'S', 'AGA' => 'R', 'AGG' => 'R', 'GTA' => 'V', 'GTC' => 'V', 'GTG' => 'V', 'GTT' => 'V', 'GCA' => 'A', 'GCC' => 'A',