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biojava-adam\n\n[Biojava](http://biojava.org) and [ADAM](https://github.com/bigdatagenomics/adam) integration.\n\n[![Build Status](https://travis-ci.org/biojava/biojava-adam.svg?branch=master)](https://travis-ci.org/biojava/biojava-adam)\n[![Maven Central](https://img.shields.io/maven-central/v/org.biojava/biojava-adam.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Corg.biojava)\n[![API Documentation](http://javadoc.io/badge/org.biojava/biojava-adam.svg?color=brightgreen\u0026label=scaladoc)](http://javadoc.io/doc/org.biojava/biojava-adam)\n\n\n### Hacking biojava-adam\n\nInstall\n\n * JDK 1.8 or later, http://openjdk.java.net\n * Apache Maven 3.6.3 or later, http://maven.apache.org\n * Apache Spark 3.2.1 or later, http://spark.apache.org\n * ADAM: Genomic Data System 1.0 or later, https://github.com/bigdatagenomics/adam\n\nTo build\n\n    $ mvn install\n\n\n### Running biojava-adam\n\nTo run interactively in `spark-shell`\n\n```\n$ spark-shell \\\n    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \\\n    --conf spark.kryo.registrator=org.biojava.nbio.adam.BiojavaKryoRegistrator \\\n    --jars target/biojava-adam-$VERSION.jar,$PATH_TO_ADAM_ASSEMBLY_JAR\n\nWelcome to\n      ____              __\n     / __/__  ___ _____/ /__\n    _\\ \\/ _ \\/ _ `/ __/  '_/\n   /___/ .__/\\_,_/_/ /_/\\_\\   version 3.2.1\n      /_/\n\nUsing Scala version 2.12.15 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191)\nType in expressions to have them evaluated.\nType :help for more information.\n\nscala\u003e import org.biojava.nbio.adam.BiojavaAdamContext\nimport org.biojava.nbio.adam.BiojavaAdamContext\n\nscala\u003e val bc = BiojavaAdamContext(sc)\nbc: org.biojava.nbio.adam.BiojavaAdamContext = org.biojava.nbio.adam.BiojavaAdamContext@4f8900b0\n\nscala\u003e val reads = bc.loadFastqReads(\"src/test/resources/org/biojava/nbio/adam/bqsr.0.fq\")\nreads: org.bdgenomics.adam.rdd.read.ReadRDD = RDDBoundReadRDD with 0 reference sequences\n\nscala\u003e reads.rdd.first\nres0: org.bdgenomics.formats.avro.Read = {\"name\": \"SRR062634.10022079/1\", \"description\":\n\"SRR062634.10022079/1\", \"alphabet\": \"DNA\", \"sequence\": \"AATTCAAAACCAGCCTGGCCAATATGGTGAAACCTCATCTCTACTAAAA\nATACAAAAATTAGCCAGGCATGGTGGTGCGTGCGTGTAGTCCCAGCTACTT\", \"length\": 100, \"qualityScores\": \"?-DDBEEB=EEEDDEDEE\nEA:D?5?E?CEBE5ED?D:AEDEDEDED-B,BC0AC,BB6@CDBDEC?BCBAA@5,=8CA-?A\u003e?2:\u0026048\u003cBB5BE#####\",\n\"qualityScoreVariant\": \"FASTQ_SANGER\", \"attributes\": {}}\n\nscala\u003e val dna = bc.loadBiojavaFastaDna(\"src/test/resources/org/biojava/nbio/adam/hla_gen.0.fa\")\ndna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences\n\nscala\u003e dna.rdd.first\nres0: org.bdgenomics.formats.avro.Sequence = {\"name\": \"HLA:HLA00001 A*01:01:01:01 3503 bp\",\n\"description\": null, \"alphabet\": \"DNA\", \"sequence\": \"CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAG\nGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTT\nCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCAC\n...\n\nscala\u003e val prot = bc.loadBiojavaFastaProtein(\"src/test/resources/org/biojava/nbio/adam/hla_prot.0.fa\")\nprot: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences\n\nscala\u003e prot.rdd.first\nres2: org.bdgenomics.formats.avro.Sequence = {\"name\": \"HLA:HLA00001 A*01:01:01:01 365 bp\", \"description\":\nnull, \"alphabet\": \"PROTEIN\", \"sequence\": \"MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSD\nAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITK\nRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVV\nPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV\", \"length\":\n365, \"attributes\": {}}\n\nscala\u003e val genbankDna = bc.loadGenbankDna(\"src/test/resources/org/biojava/nbio/adam/SCU49845.gb\")\ngenbankDna: org.bdgenomics.adam.rdd.sequence.SequenceRDD = RDDBoundSequenceRDD with 0 reference sequences\n\nscala\u003e genbankDna.rdd.first\nres4: org.bdgenomics.formats.avro.Sequence = {\"name\": \"U49845\", \"description\": \"Saccharomyces cerevisiae\nTCP1-beta gene, partial cds; and Axl2p\\n(AXL2) and Rev7p (REV7) genes, complete cds.\", \"alphabet\": \"DNA\",\n\"sequence\": \"GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGT\nTACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAA\nCATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAG\n...\n\nscala\u003e val features = bc.loadGenbankDnaFeatures(\"src/test/resources/org/biojava/nbio/adam/SCU49845.gb\")\nfeatures: org.bdgenomics.adam.rdd.feature.FeatureRDD = RDDBoundFeatureRDD with 0 reference sequences\n\nscala\u003e features.rdd.first\nres5: org.bdgenomics.formats.avro.Feature = {\"featureId\": null, \"name\": \"source\", \"source\": null,\n\"featureType\": null, \"contigName\": \"U49845\", \"start\": 0, \"end\": 5028, \"strand\": \"FORWARD\", \"phase\":\nnull, \"frame\": null, \"score\": null, \"geneId\": null, \"transcriptId\": null, \"exonId\": null, \"aliases\":\n[], \"parentIds\": [], \"target\": null, \"gap\": null, \"derivesFrom\": null, \"notes\": [], \"dbxrefs\": [],\n\"ontologyTerms\": [], \"circular\": null, \"attributes\": {}}\n```\n\n\n### Example biojava-adam scripts\n\nSome scripts for `spark-shell` written in Scala are provided in the `scripts` directory. E.g. to transform\nDNA sequences in Genbank format to `Sequence`s in Parquet format:\n\n```\n$ INPUT=Homo_sapiens.GRCh38.96.chromosome.21.dat.gz \\\n  OUTPUT=Homo_sapiens.GRCh38.96.chromosome.21.sequences.adam \\\n  spark-shell \\\n    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \\\n    --conf spark.kryo.registrator=org.biojava.nbio.adam.BiojavaKryoRegistrator \\\n    --jars target/biojava-adam-$VERSION.jar,$PATH_TO_ADAM_ASSEMBLY_JAR\n    -i scripts/loadGenbankDna.scala\n```\n\nAll the scripts follow a similar pattern, with input path specified by `INPUT` environment variable and output\npath specified by `OUTPUT` environment variable.\n","funding_links":[],"categories":["Extending ADAM"],"sub_categories":["Libraries"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojava%2Fbiojava-adam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiojava%2Fbiojava-adam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojava%2Fbiojava-adam/lists"}