Nullpointerexception when reading a sequence with ambiguous DNA nucleotide #191
Description
I have been banging my head over this, but I can't seem to figure out why it's going wrong.
It specifically happens on this sequence in the file:
>gb:GQ903697|Organism:Arenavirus H0030026 H0030026|Segment:S|Host:Rat
CGCACAGAGGATCCTAGGCGTTACTGACTTGCGCTAATAACAGATACTGTTTCATATTTAGATAAAGACC
CAGCCAACTGATTGGTCAGCATGGGACAACTTGTGTCCCTCTTCAGTGAAATTCCATCAATCATACACGA
AGCTCTCAATGTTGCTCTCGTAGCTGTTAGCATCATTGCAATATTGAAAGGGGTTGTGAATGTTTGGAAG
AGTGGAGTTTTGCAGCTTTTGGCCTTCTTGCTCCTGGCGGGAAGATCCTGCTCAGTCATAATTGGTCATC
ATCTCGAACTGCAGCATGTGATCTTCAATGGGTCATCAATCACACCCTTTTTACCAGTTACATGTAAGAT
CAATGATACCTACTTCCTACTAAGAGGCCCCTATGAAGCTGATTGGGCAGTTGAATTGAGTGTAACTGAA
ACCACAGTCTTGGTTGATCTTGAAGGTGGCAGCTCAATGAAGCTGAAAGCCGGAAACATCTCAGGTTGTC
TTGGAGACAACCCCCATCTGAGATCAGTGGTCTTCACATTGAATTGGTTGCTAACAGGATTAGATCATGT
TATTGATTCTGACCCGAAAATTCTCTGTGATCTTAAAGACAGTGGGCACTTTCGTCTCCAGATGAACTTA
ACAGAAAAGCACTATTGTGACAAGTTTCACATCAAAATGGGCAAGGTCTTTGGCGTATTCAAAGATCCGT
GCATGGCTGGTGGTAAAATGTTTGCCATACTAAAAAATACCTCTTGGTCGAACCAGTGCCAAGGAAACCA
TGTCAGCACCATTCATCTTGTCCTTCAGAGTAATTTCAAACAGGTCCTCAGTAGCAGGAAACTGTTGAAC
TTTTTCAGCTGGTCATTGTCTGATGCCACAGGGGCTGATATGCCTGGTGGTTTTTGTCTGGAAAAATGGA
TGTTGATTTCAAGTGAACTGAAATGCTTTGGAAACACAGCTGTGGCAAAGTGCAACTTAAATCATGACTC
AGAGTTCTGTGACATGCTTAGGCTTTTTGATTTCAACAAAAAGGCAATAGTCACTCTTCAGAACAAAACA
AAGCATCGGCTGGACACAGTAATTACTGCTATCAATTCATTGATCTCTGATAATATTCTTATGAAGAACA
GGATTAAAGAATTGATAGATGTTCCTTACTGTAATTACACCAAATTTTGGTATGTCAATCACACAGGTCT
AAATCTGCACACCCTTCCAAGATGTTGGCTTGTTAAAAATGGTAGCTACTTGAATGTGTCTGACTTCAGG
AATGAGTGGATATTGGAGAGTGATCATCTTGTTTCGGAGATCCTTTCAAAGGAGTATGAGGAAAGGCAAA
ATCGTACACCACTCTCACTGGTTGACATCTGTTTCTGGAGTACATTGTTTTACACAGCATCAATTTTCCT
ACACCTCTTGAGAATTCCAACCCACAGACACATTGTTGGTGAGGGCTGCCCGAAGCCTCATAGGCTAAAC
AGGCACTCAATATGTGCTTGTGGCCTTTTCAAACAAGAAGGCAGACCCTTGAGATGGGTAAGAAAGGTGT
GAACAATGGTTGCTTGGTGGCCTCCATTGCTGCACCCCCCTAGGGGGGTGCAGCAATGGAGGTTCTCGYT
GAGCCTAGAGAACAACTGTTGAATCGGGTTCTCTAAAGAGAACATCGATTGGTAGTACCCTTTTTGGTTT
TTCATTGGTCACTGACCCTGAAAGCACAGCACTGAACATCAAACAGTCCAAAAGTGCACAGTGTGCATTT
GTTGTGGCTGGTGCTGATCCTTTCTTCTTACTTTTAATGACTATTCCCTTATGTCTGTCACACAGATGTT
CAAATCTCTTCCAAACAAGATCTTCAAAGAGCCGTGACTGTTCTGCGGTCAGTTTGACATCAACAATCTT
CAAATCCTGTCTTCCATGCATATCAAAGAGCCTCCTAATATCATCAGCACCTTGCGCAGTGAAAACCATG
GATTTAGGCAGACTCCTTATTATGCTTGTGATGAGGCCAGGTCGTGCATGTTCAACATCCTTCAGCAATA
TCCCATGACAATATTTACTTTGGTCCTTAAAAGATTTTATGTCATTGGGTTTTCTGTAGCAGTGGATGAA
TTTTTGTGATTCAGGCTGGTAAATTGCAAACTCAACAGGGTCATGTGGCGGGCCTTCAATGTCAATCCAT
GTTGTGTCACTGACCATCAACGACTCTACACTTCTCTTCACCTGAGCCTCCACCTCAGGCTTGAGCGTGG
ACAAGAGTGGGGCACCACCGTTCCGGATGGGGACTGGTGTTTTGCTTGGTAAACTCTCAAATTCCACAAC
TGTATTGTCCCATGCTCTCCCTTTGATCTGTGATCTTGATGAAATGTAAGGCCAGCCCTCACCAGAGAGA
CACACCTTATAAAGTATGTTTTCATAAGGATTCCTCTGTCCTGGTATGGCACTGATGAACATGTTTTCCC
TCTTTTTGATCTCCAAGAGGGTTTTTATAATGGTTGTGAATGTGGACTCCTCAATCTTTATTGTTTCCAG
CATGTTGCCACCATCAATCAGGCAAGCACCGGCTTTCACAGCAGCTGATAAACTAAGGTTGTAGCCTGAT
ATGTTAATTTGAGAATCCTCCTGAGTGATTACCTTTAGAGAAGGATGCTTCTCCATCAAAGCATCTAAGT
CACTTAAATTAGGGTATTTTGCTGTGTATAGCAACCCCAGATCTGTGAGGGCCTGAACCACATCATTTAG
AGTTTCCCCTCCCTGTTCAGTCATACAGGAAATTGTGAGTGCTGGCATCGATCCAAATTGGTTGATCATA
AGTGATGAGTCTTTAACGTCCCAGACTTTGACCACCCCTCCAGTTCTAGCCAACCCAGGTCTCTGAATAC
CAACAAGTTGCAGAATTTCGGACCTCCTGGTGAGCTGTGTTGTAGAGAGGTTCCCTAGATACTGGCCACC
TGTGGCTGTCAACCTCTCTGTTCTTTGAACTTTTTGCCTTAATTTGTCCAAGTCACTGGAGAGTTCCATT
AGCTCTTCCTTTGACAATGATCCTATCTTAAGGAACATGTTCTTTTGGGTTGACTTCATGACCATCAATG
AGTCAACTTCCTTATTCAAGTCCCTCAAACTAACAAGATCACTGTCATCTCTTTTAGACCTCCTCATCAT
GCGTTGCACACTTGCAACCTTTGAAAAATCTAAGCCGGACAGAAGAGCCCTCGCGTCAGTTAGGACATCT
GCCTTAACAGCAGTTGTCCAGTTCGAGAGTCCTCTCCTGAGAGACTGTGTCCATCTGAATGATGGGATTG
GTTGTTCGCTCATAGTGATGAAATTGCGCAGAGTTATCCAAAAGCCTAGGATCCTCTGTGCG
This is the first sequence in my file that includes the ambiguous nucleotide "Y".
I use this code to read and process the file:
public class Something {
public static void main(String[] args) throws Exception {
File file = new File("my.genomic.fasta");
FastaReader<DNASequence, NucleotideCompound> proxy =
new FastaReader<DNASequence, NucleotideCompound>(
file,
new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String, DNASequence> dnaSequences = proxy.process();
for (DNASequence dna : dnaSequences.values()) {
TranscriptionEngine engine = TranscriptionEngine.getDefault();
Frame[] sixFrames = Frame.getAllFrames();
// Nullpointer exception below
Map<Frame, Sequence<AminoAcidCompound>> results = engine.multipleFrameTranslation(dna, sixFrames);
}
}
}It processes the first few sequences in that file, until it gets to the sequence above. Then I get this exception:
Exception in thread "main" java.lang.NullPointerException
at org.biojava3.core.sequence.template.AbstractCompoundTranslator.createSequences(AbstractCompoundTranslator.java:95)
at org.biojava3.core.sequence.transcription.DNAToRNATranslator.createSequences(DNAToRNATranslator.java:53)
at org.biojava3.core.sequence.template.AbstractCompoundTranslator.createSequence(AbstractCompoundTranslator.java:160)
at org.biojava3.core.sequence.transcription.DNAToRNATranslator.createSequence(DNAToRNATranslator.java:89)
at org.biojava3.core.sequence.transcription.TranscriptionEngine.multipleFrameTranslation(TranscriptionEngine.java:131)
at Something.main(Something.java:33)
What's causing this?