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This article mainly introduces bioperl how to read and write fasta/fastq compressed files, the article is very detailed, has a certain reference value, interested friends must read it!

Bioperl reads and writes fasta/fastq compressed files

Bioperl reads and writes fasta/fastq files in gz compressed format as follows:

Enter the file handle:

Fastq file

Open my $FQ, "zcat infile.fq.gz |" or die "$!"

My$fq=Bio::SeqIO- > new (- fh= > $FQ,-format= > 'fastq')

Fasta file

Open my $FA, "zcat infile.fa.gz |" or die "$!"

My$fa=Bio::SeqIO- > new (- fh= > $FA,-format= > 'fasta')

Output file handle:

Fastq file

Open my $GZ, "| gzip > outfile.fq.gz" or die $!

My$out = Bio::SeqIO- > new (- fh = > $GZ,-format = > 'fastq')

Fasta file

Open my $GZ, "| gzip > outfile.fa.gz" or die $!

My$out = Bio::SeqIO- > new (- fh = > $GZ,-format = > 'fasta')

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