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 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";

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