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loadFastaDna.scala
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48 lines (35 loc) · 1.74 KB
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/*
biojava-adam BioJava and ADAM integration.
Copyright (c) 2017-2022 held jointly by the individual authors.
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
*/
import org.slf4j.LoggerFactory
val logger = LoggerFactory.getLogger("loadFastaDna")
import org.apache.log4j.{ Level, Logger }
Logger.getLogger("loadFastaDna").setLevel(Level.INFO)
Logger.getLogger("org.biojava").setLevel(Level.INFO)
import org.biojava.nbio.adam.BiojavaAdamContext
val bac = BiojavaAdamContext(sc)
val inputPath = Option(System.getenv("INPUT"))
val outputPath = Option(System.getenv("OUTPUT"))
if (inputPath.isEmpty || outputPath.isEmpty) {
logger.error("INPUT and OUTPUT environment variables are required")
System.exit(1)
}
val sequences = bac.loadBiojavaFastaDna(inputPath.get)
logger.info("Saving DNA sequences to output path %s ...".format(outputPath.get))
sequences.save(outputPath.get, asSingleFile = true, disableFastConcat = false)
logger.info("Done")
System.exit(0)