bioperl处理fasta序列最全代码：
序列的读取与输出
use Bio::SeqIO;
use Bio::Seq;
use Data::Dumper;
$in = Bio::SeqIO->new(-file => "D:/share/scripts/Arabidopsis_thaliana.TAIR10.cds.all.fa" ,
-alphabet=>"dna",
-format => 'Fasta');
$out = Bio::SeqIO->new(-file => ">D:/share/scripts/aa.fa" ,
-format => 'fasta');
while ( my $seqobj = $in->next_seq() ) {
# the human read-able id of the sequence
my $id=$seqobj->id();
# string of sequence
my $seq=$seqobj->seq();
# a description of the sequence
my $desc=$seqobj->desc();
# one of 'dna','rna','protein' https://www.bioinformatics.org/sms/iupac.html
my $alphabet=$seqobj->alphabet();
my $len=$seqobj->length();
print $id."\n";
print $seq."\n";
print $desc."\n";
print $alphabet."\n";
print $len."\n";
print $seqobj."\n";
print Dumper($seqobj);
$out->write_seq($seqobj);
last;
}
Fastq序列的处理：
$in1 = Bio::SeqIO->new(-file => "D:/share/scripts/test_1.fastq" ,
-format => 'fastq');
$in2 = Bio::SeqIO->new(-file => "D:/share/scripts/test_2.fastq" ,
-format => 'fastq');
$out = Bio::SeqIO->new(-file => ">D:/share/scripts/test_1.fa" ,
-format => 'fasta');
while ( my $seqobj1 = $in1->next_seq() and my $seqobj2 = $in2->next_seq()) {
# the human read-able id of the sequence
my $id=$seqobj->id();
# string of sequence
my $seq=$seqobj->seq();
# a description of the sequence
my $desc=$seqobj->desc();
# one of 'dna','rna','protein' https://www.bioinformatics.org/sms/iupac.html
my $alphabet=$seqobj->alphabet();
my $len=$seqobj->length();
my $qual=$seqobj->qual();
print $id."\n";
print $seq."\n";
print $desc."\n";
print $alphabet."\n";
print $len."\n";
print "@{$qual}\n";
print Dumper($seqobj);
$out->write_seq($seqobj);
last;
}
序列的截取 反向互补序列：
my$seqobj = Bio::Seq->new(-seq => 'actgtggcgtcaact',-desc => 'Sample Bio::Seq object',-id =>"ID1");
# part of the sequence as a string
my$subseq=$seqobj->subseq(5,10);
print $subseq."\n";
my $newSeqobj = Bio::Seq->new(-seq => $subseq,
-desc => 'subseq 5-10',
-id =>"ID2",
);
$out->write_seq($newSeqobj);
trunc和subseq有区别，trunc返回还是原来的序列对象，只是截短了，而subseq返回的是截取的序列字符串，一般subseq使用的多一些：
$out = Bio::SeqIO->new(-file => ">D:/share/scripts/subseq1.fa" ,
-format => 'Fasta');
my$subseqObj= $seqobj->trunc(5,10);
my$subseq=$seqobj->subseq(5,10);
print $subseqObj."\n";
print $subseq."\n";
$out->write_seq($subseqObj);
my$revcom= $seqobj->revcom; #序列反向互补
print $revcom."\n";
print $subseqObj."\n";
print $seqobj."\n";
DNA序列翻译成蛋白质序列：
#参数 1 stop *
# 2 unknown amino acid ('X').
my$translate0=$seqobj->translate(undef,undef,0);
my$translate1=$seqobj->translate(undef,undef,1);
my$translate2=$seqobj->translate(undef,undef,2);
print Dumper($translate0)."\n";
print Dumper($translate1)."\n";
print Dumper($translate2)."\n";
推荐学习《perl高级编程》，有bioperl的详细讲解；
