How to read a FASTA fie with FastaReaderTeat.java?

If you compiled the example program, FastaReaderTeat.java, with Maven as shown in the previous tutorial, you can follow these steps to read a FASTA file.

1. Prepare a FASTA file, example.fasta.

fyicenter$ cd bio 
fyicenter$ vi example.fasta 

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10
FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK

2. Run FastaReaderTeat.java with BioJava Core JAR file.

fyicenter$ java -cp target/bio-1.0.jar:$Core_JAR com.fyicenter.FastaReaderTeat example.fasta 

Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
  at org.biojava.nbio.core.sequence.io.FastaReader.<clinit>(FastaReader.java:46)
  at com.fyicenter.FastaReaderTeat.main(FastaReaderTeat.java:30)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
  at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
  at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
  at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)

3. Add SLF4J JAR file into the class path and run it again.

fyicenter$ export SLF4J_JAR=/home/fyicenter/.m2/repository/org/slf4j/slf4j-api/1.7.30/slf4j-api-1.7.30.jar

fyicenter$ java -cp target/bio-1.0.jar:$Core_JAR:$SLF4J_JAR com.fyicenter.FastaReaderTeat example.fasta 

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

1 : seq0 FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
2 : seq2 EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
3 : seq3 MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
4 : seq4 EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
5 : seq5 SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
6 : seq6 FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
7 : seq7 SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
8 : seq8 SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
9 : seq9 KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
10 : seq10 FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK

As you can see, FastaReaderTeat.java is able to read a FASTA file. But "seq1" seqence is missing in the output, and the SLF4J implementation JAR is also missing. See next tutorial on how to build the class path properly with Maven.

⇒ "mvn dependency:build-classpath" - Generate Class Pass

⇐ Use BioJava with "Maven" Build Tool

⇑ BioJava - Java Bioinformatics Toolkit

⇑⇑ OBF (Open Bioinformatics Foundation) Tools