Convert the output from hml-to-sequence and create a FASTA file
Requires Java 8 and Maven
mvn clean install
This script takes the sequence (txt) output from hml2seq and formats it into a FASTA file for downstream usage with SeqAnn.
java -jar target/hla2fasta-1.0-SNAPSHOT.jar sequences.txt
The output files are divided by loci (denoted by filename suffixes) and appear in the working directory. For example, having a sequences.txt input file will create sequences_A.txt, sequences_B.txt, etc...
The functionality of this program is verified through BDD (behavior-driven development). JBehave is used to facilitate BDD tests. To check the status of tests ran through Maven, check target/jbehave/view/reports.html.