Bioperl使用

测序文件读入写出

use Bio::SeqIO;
use Bio::Seq;
use Data::Dumper;

#fasta
$in = Bio::SeqIO->new(-file => "D:/test.fa", -format => 'Fasta', -alphabet =>"dna");
$out = Bio::SeqIO->new(-file => ">D:/aa.fa", -format => 'EMBL');

while (my$seqobj = $in->next_seq()){
	my $id = $seqobj->id(); 	#the human read-able id of the sequence
	my $seq = $seqobj->seq();	#string of sequence
	my $desc = $seqobj->desc();	#a description of the sequence
	my $alphabet = $seqobj->alphabet();	#one of 'dna', 'rna', 'protein'
	my $len = $seqobj->length();

	print $seqobj."\n";
	print Dumper($seqobj);
	$out->write_seq($seqobj);  #实现格式转换
	
	last;	#只读一条序列
}

#fastq双端
$in1 = Bio::SeqIO -> new(-file =>"D:/test_1.fq", -format => 'fastq');
$in2 = Bio::SeqIO -> new(-file =>"D:/test_2.fq", -format => 'fastq');
$out = Bio::SeqIO->new(-file => ">D:/test_1.fa", -format => 'fasta');

while (my $seqobj1 = $in1 ->next_seq() and my $seqobj2 = $in2 -> next_seq()){
	my ($id1, $id2) = ($seqobj1->id, $seqobj2->id); 	
	my ($seq1,$seq2) = ($seqobj1->seq, $seqobj2->seq);	
	my ($desc1,$desc2) = ($seqobj1->desc, $seqobj2 ->desc);	
	my ($alphabet1, $alphabet2) = ($seqobj1->alphabet, $seqobj2->alphabet);	#one of 'dna', 'rna', 'protein'
	my ($len1,$len2) = ($seqobj1->length, $seqobj2 ->length);
	my ($qual1, $qual2) = ($seqobj1->qual,$seqobj2->qual);

	$out->write_seq($seqobj1,$seqobj2);
	last;
}

write_seq()只能传入bioseq对象，接收字符串会报错

序列截取

#创建bioseq对象
$seqobj = Bio::Seq->new(-seq => "aaccggtt", -desc => "Sample Bio::Seq object", -id => "ID1");
$out = Bio::SeqIO->new(-file =>">./subseq.fa", -format=>"Fasta");

#subseq截取，返回字符串
my $subseq = $seqobj->subseq(3,5);
#注意：这里的索引从1开始，所以截取3-5获得的序列是: ccg
print $subseq."\n";

my$newseqobj = Bio::Seq ->new(-seq=$subseq, -desc=>"subseq 3-5", -id="ID2");
$out->write_seq($newseqobj);

#trunc截取，返回bioseq对象，desc和id信息不变
my$subseqobj = $seqobj->trunc(3,5);
$out->write_seq($subseqobj);

反向互补序列

my$revcom = $seqobj ->revcom;返回bioseq对象

蛋白质翻译

my$translate = $seqobj->translate(undef,undef,0);
translate第一个参数stop符号，默认*；第二个参数unknown amino acid (‘X’)；第三个参数开始位置，比如0，1，2