bioperl怎么处理fasta和fastq序列

bioperl怎么处理fasta和fastq序列

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bioperl处理fasta序列最全代码：

序列的读取与输出

useBio::SeqIO;useBio::Seq;useData::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()){#thehumanread-ableidofthesequencemy$id=$seqobj->id();#stringofsequencemy$seq=$seqobj->seq();#adescriptionofthesequencemy$desc=$seqobj->desc();#oneof'dna','rna','protein'https://www.bioinformatics.org/sms/iupac.htmlmy$alphabet=$seqobj->alphabet();my$len=$seqobj->length();print$id."\n";print$seq."\n";print$desc."\n";print$alphabet."\n";print$len."\n";print$seqobj."\n";printDumper($seqobj);$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=$in1->next_seq()andmy$seqobj2=$in2->next_seq()){#thehumanread-ableidofthesequencemy$id=$seqobj->id();#stringofsequencemy$seq=$seqobj->seq();#adescriptionofthesequencemy$desc=$seqobj->desc();#oneof'dna','rna','protein'https://www.bioinformatics.org/sms/iupac.htmlmy$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"@{$qual}\n";printDumper($seqobj);$out->write_seq($seqobj);last;}

序列的截取 反向互补序列：

my$seqobj=Bio::Seq->new(-seq=>'actgtggcgtcaact',-desc=>'SampleBio::Seqobject',-id=>"ID1");#partofthesequenceasastringmy$subseq=$seqobj->subseq(5,10);print$subseq."\n";my$newSeqobj=Bio::Seq->new(-seq=>$subseq,-desc=>'subseq5-10',-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);printDumper($translate0)."\n";printDumper($translate1)."\n";printDumper($translate2)."\n";

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