bioperl读写gz压缩格式的fasta/fastq文件方法如下:
输入文件句柄:
fastq文件
open my F Q , " z c a t i n f i l e . f q . g z ∣ " o r d i e " FQ ,"zcat infile.fq.gz|" or die " FQ,"zcatinfile.fq.gz∣"ordie"!";
my f q = B i o : : S e q I O − > n e w ( − f h = > fq=Bio::SeqIO->new(-fh=> fq=Bio::SeqIO−>new(−fh=>FQ,-format=>‘fastq’);
fasta文件
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fa=Bio::SeqIO->new(-fh=>
fa=Bio::SeqIO−>new(−fh=>FA,-format=>‘fasta’);
输出文件句柄:
fastq文件
open my $GZ ,"| gzip >outfile.fq.gz" or die $!;
my$out = Bio::SeqIO->new(-fh => $GZ , -format => ‘fastq’);
fasta文件
open my $GZ ,"| gzip >outfile.fa.gz" or die $!;
my$out = Bio::SeqIO->new(-fh => $GZ , -format => ‘fasta’);