java 生物信息学_生物信息学java库

生物信息学文件处理库

最新推荐文章于 2024-08-20 09:33:29 发布

原创最新推荐文章于 2024-08-20 09:33:29 发布 · 237 阅读

0 ·

CC 4.0 BY-SA版权

文章标签：

#java 生物信息学

介绍了一个用于生物信息学文件处理的库，支持FASTA、FASTQ等格式，强调了性能与内存使用效率，提供了不可变对象以确保数据一致性。

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