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

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 sequencemy $id=$seqobj->id();  # string of sequencemy $seq=$seqobj->seq();# a description of the sequencemy $desc=$seqobj->desc(); # one of '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 $seqobj."\n";print Dumper($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 sequencemy $id=$seqobj->id(); # string of sequencemy $seq=$seqobj->seq(); # a description of the sequencemy $desc=$seqobj->desc(); # one of '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";print Dumper($seqobj);$out->write_seq($seqobj);last;}

序列的截取 反向互补序列：

my$seqobj = Bio::Seq->new(-seq => 'actgtggcgtcaact',-desc => 'Sample Bio::Seq object',-id =>"ID1");# part of the sequence as a stringmy$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";

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