Biojava - import org.biojava.bio in maven
I want to read multiple FASTA sequences from a FASTA file in Java. I found that BioJava can help with that(Eg:Solution 1): http://biojava.org/wiki/BioJava%3ACookbook%3ASeqIO%3AReadFasta
However, I am getting an error saying "Package org.biojava.bio does not exist" even though I imported following packages in maven:
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>4.2.4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-ws</artifactId>
<version>4.2.4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>4.2.4</version>
</dependency>
My Questions are:
- What is the dependency missing here?
- is BioJava outdated? Why so many "Page not found" ? if so, what is the latest java library for bioinformatics?
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1 answer
BioJava recently had to change the website to a new hosting, and the wiki-pages are not yet full up-to-date. The page you are looking it is a BioJava1 - example.
In BioJava 3 and newer, check out the FastaReaderHelper class. Here a link to the BioJava tutorial:
https://github.com/biojava/biojava-tutorial/blob/master/core/readwrite.md
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