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Parsing of FASTA header into name and description differs from ADAM #2

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heuermh opened this issue Feb 2, 2018 · 0 comments
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heuermh commented Feb 2, 2018

scala>  import org.biojava.nbio.adam.BiojavaAdamContext
scala>  val biojavaContext = new BiojavaAdamContext(sc)

scala> val dna = sc.loadBiojavaFastaDna("../adam/adam-core/src/test/resources/HLA_DQB1_05_01_01_02.fa")
scala> val dna = biojavaContext.loadBiojavaFastaDna("../adam/adam-core/src/test/resources/HLA_DQB1_05_01_01_02.fa")

scala> dna.rdd.first

res6: org.bdgenomics.formats.avro.Sequence = {
"name": "HLA-DQB1*05:01:01:02\tHLA06615 7090 bp", "description": null,
"alphabet": "DNA", "sequence": "TTCTAAGACCTTTGCTCTTCTCCCCAGGACTTAAGGCTCTTCAGCGTGTCTAAGACAACAGCAGTAAAAATTTCTGTGACAGCAATTTTCTCTCCCCTGAAATATGATCCCCACCTAATTTGCTTTATTAAAAATCCCAAGTATAATAACAACTGGTTTTTAACAATATTACAGAGATGTTTACTGTTGAATTGCATTTTTCTTTTGCCTCTCAAAATCCCTGAGGAATTTGTTCTTCAGCTCTTCTATAATCGAGAGGAAATTTTCACCTCAGATGTTCATCCAGTGCAATTGGAAGACGTCACAGTGCCAGGCACTGGATTGAGAACCTTCACAAAAAAAAATGTCTGCCCAGAGACAGATGAGGTCCTTCAGCTCCAGTGCTGATTGGTTCTTTTCCAAGCGACCATCCAATCCTGCCACGCACGGAAACATCCACAGGTTTTTATTCTTTCTGCCAGGTACATCAGATCCATCAGGTCTGAGCTGTGTTGACTACCACTACTTTTCCCTTCGTCTCAATTATGTCTTGGAAGAAGTCTTTGCGGATCCCCGGAGACCTTCGGGTAGCAACTGTCACCTTGATGCTGGCGATCCTGAGCTCCTCACTGGCTGAGGGCAGAGACTCTCCCGGTAAGTGCAGGAAAG...

scala> val dna = biojavaContext.loadFastaDna("../adam/adam-core/src/test/resources/HLA_DQB1_05_01_01_02.fa")

scala> dna.rdd.first

res8: org.bdgenomics.formats.avro.Sequence = {
"name": "HLA-DQB1*05:01:01:02", "description": "HLA06615 7090 bp",
"alphabet": "DNA", "sequence": "TTCTAAGACCTTTGCTCTTCTCCCCAGGACTTAAGGCTCTTCAGCGTGTCTAAGACAACAGCAGTAAAAATTTCTGTGACAGCAATTTTCTCTCCCCTGAAATATGATCCCCACCTAATTTGCTTTATTAAAAATCCCAAGTATAATAACAACTGGTTTTTAACAATATTACAGAGATGTTTACTGTTGAATTGCATTTTTCTTTTGCCTCTCAAAATCCCTGAGGAATTTGTTCTTCAGCTCTTCTATAATCGAGAGGAAATTTTCACCTCAGATGTTCATCCAGTGCAATTGGAAGACGTCACAGTGCCAGGCACTGGATTGAGAACCTTCACAAAAAAAAATGTCTGCCCAGAGACAGATGAGGTCCTTCAGCTCCAGTGCTGATTGGTTCTTTTCCAAGCGACCATCCAATCCTGCCACGCACGGAAACATCCACAGGTTTTTATTCTTTCTGCCAGGTACATCAGATCCATCAGGTCTGAGCTGTGTTGACTACCACTACTTTTCCCTTCGTCTCAATTATGTCTTGGAAGAAGTCTTTGCGGATCCCCGGAGACCTTCGGGTAGCAACTGTCACCTTGATGCTGGCGATCCTGAGCTCCTCACTGGCTGAGGGCAGAGACTCTCCCGGTAAGTGCAGGAAAGCTGC...
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