这篇文章主要介绍“bioperl怎么处理fasta和fastq序列”的相关知识,小编通过实际案例向大家展示操作过程,操作方法简单快捷,实用性强,希望这篇“bioperl怎么处理fasta和fastq序列”文章能帮助大家解决问题。
bioperl处理fasta序列最全代码:
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; }
$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; }
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 $seqobj."\n";
#参数 1 stop *
# 2 unknown amino acid ('X').
my$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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