bioperl怎么處理fasta和fastq序列

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bioperl處理fasta序列最全代碼：

序列的讀取與輸出

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序列的處理：

$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  反向互補序列：

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有區別，trunc返回還是原來的序列對象，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;  #序列反向互補
print   $revcom."\n";
print $subseqObj."\n";
print   $seqobj."\n";

DNA序列翻譯成蛋白質序列：

#參數   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";

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