java 生物信息学_生物信息学java库

Library and Tools for bioinformatics file manipulation, including fasta, fastQ, gff and vcf formats.

The library follow some principles:

You need performance and need to save memory

You can't/don't want to put everything in memory

Objects are immutables

Documentation is available.

I tried to use biojava, but version 2 is too complex and version 3 has some problems, for exemple, this is the code to read a fasta file:

FastaReader fastaReader = new FastaReader(inStream, new GenericFastaHeaderParser(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));LinkedHashMap b = fastaReader.process();for ( Entry entry : b.entrySet() ) {System.out.println( entry.getVal