Added tool to download a NCBI assembly

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.{File, PrintWriter}
+
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.io.Source
+
+/**
+  * Created by pjvan_thof on 21-9-16.
+  */
+object DownloadNcbiAssemblyextends extends ToolCommand {
+
+  case class Args(assemblyId: File = null,
+                  outputFile: File = null,
+                  contigNameHeader: Option[String] = None,
+                  mustHaveOne: Map[String, String] = Map(),
+                  mustNotHave: Map[String, String] = Map()) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('a', "assembly id") required () valueName "<file>" action { (x, c) =>
+      c.copy(assemblyId = x)
+    }
+    opt[File]('o', "output") required () valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = x)
+    }
+    opt[String]("nameHeader") valueName "<string>" action { (x, c) =>
+      c.copy(contigNameHeader = Some(x))
+    }
+    opt[(String, String)]("mustHaveOne") valueName "<string>" action { (x, c) =>
+      c.copy(mustHaveOne = c.mustHaveOne + (x._1 -> x._2))
+    }
+    opt[(String, String)]("mustNotHave") valueName "<string>" action { (x, c) =>
+      c.copy(mustNotHave = c.mustNotHave + (x._1 -> x._2))
+    }
+  }
+
+  /**
+    * @param args the command line arguments
+    */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdargs: Args = argsParser.parse (args, Args () ) getOrElse (throw new IllegalArgumentException)
+
+    logger.info(s"Reading ${cmdargs.assemblyId} from NCBI")
+    val reader = Source.fromURL(s"ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/${cmdargs.assemblyId}.assembly.txt")
+    val assamblyReport = reader.getLines().toList
+    reader.close()
+
+    val headers = assamblyReport.filter(_.startsWith("#")).last.stripPrefix("# ").split("\t").zipWithIndex.toMap
+    val nameId = cmdargs.contigNameHeader.map(x => headers(x))
+    val lengthId = headers.get("Sequence-Length")
+
+    val baseUrlEutils = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
+
+    val fastaWriter = new PrintWriter(cmdargs.outputFile)
+
+    val allContigs = assamblyReport.filter(!_.startsWith("#"))
+      .map(_.split("\t"))
+    val totalLength = lengthId.map(id => allContigs.map(_.apply(id).toLong).sum)
+
+    logger.info(s"${allContigs.size} contigs found")
+    totalLength.foreach(l => logger.info(s"Total length: ${l}"))
+
+    val filterContigs = allContigs
+      .filter(values => cmdargs.mustNotHave.forall(x => values(headers(x._1)) != x._2))
+      .filter(values => cmdargs.mustHaveOne.exists(x => values(headers(x._1)) == x._2) || cmdargs.mustHaveOne.isEmpty)
+    val filterLength = lengthId.map(id => filterContigs.map(_.apply(id).toLong).sum)
+
+    logger.info(s"${filterContigs.size} contigs left after filtering")
+    filterLength.foreach(l => logger.info(s"Filtered length: ${l}"))
+
+    filterContigs.foreach { values =>
+        val id = if (values(6) == "na") values(4) else values(6)
+        logger.info(s"Start download ${id}")
+        val fastaReader = Source.fromURL(s"${baseUrlEutils}/efetch.fcgi?db=nuccore&id=${id}&retmode=text&rettype=fasta")
+        fastaReader.getLines()
+          .map(x => nameId.map(y => x.replace(">", s">${values(y)} ")).getOrElse(x))
+          .foreach(fastaWriter.println)
+        fastaReader.close()
+      }
+
+    logger.info("Downloading complete")
+
+    fastaWriter.close()
+
+  }
+}