diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FASTAInFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FASTAInFormatter.scala new file mode 100644 index 0000000000..203b93f86a --- /dev/null +++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FASTAInFormatter.scala @@ -0,0 +1,70 @@ +/** + * Licensed to Big Data Genomics (BDG) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The BDG licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.bdgenomics.adam.rdd.sequence + +import java.io.OutputStream +import org.apache.hadoop.conf.Configuration +import org.bdgenomics.adam.rdd.{ InFormatter, InFormatterCompanion } +import org.bdgenomics.adam.sql.{ Sequence => SequenceProduct } +import org.bdgenomics.formats.avro.Sequence + +/** + * InFormatter companion that creates an InFormatter that writes FASTA. + */ +object FASTAInFormatter extends InFormatterCompanion[Sequence, SequenceProduct, SequenceDataset, FASTAInFormatter] { + + /** + * Builds a FASTAInFormatter to write FASTA. + * + * @param gDataset GenomicDataset of Sequences. Used to get HadoopConfiguration. + * @return Returns a new FASTA InFormatter. + */ + def apply(gDataset: SequenceDataset): FASTAInFormatter = { + new FASTAInFormatter(gDataset.rdd.context.hadoopConfiguration) + } +} + +class FASTAInFormatter private ( + conf: Configuration) extends InFormatter[Sequence, SequenceProduct, SequenceDataset, FASTAInFormatter] { + + protected val companion = FASTAInFormatter + private val lineWidth = conf.getInt(SequenceDataset.FASTA_LINE_WIDTH, 60) + + /** + * Writes sequences to an output stream in FASTA format. + * + * @param os An OutputStream connected to a process we are piping to. + * @param iter An iterator of records to write. + */ + def write(os: OutputStream, iter: Iterator[Sequence]) { + def toFasta(sequence: Sequence): String = { + val sb = new StringBuilder() + sb.append(">") + sb.append(sequence.getName) + Option(sequence.getDescription).foreach(n => sb.append(" ").append(n)) + sequence.getSequence.grouped(lineWidth).foreach(line => { + sb.append("\n") + sb.append(line) + }) + sb.append("\n") + sb.toString + } + + iter.foreach(sequence => os.write(toFasta(sequence).getBytes)) + } +} diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala index d629879308..8361f02f51 100644 --- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala +++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala @@ -74,6 +74,12 @@ private[adam] class SequenceArraySerializer extends IntervalArraySerializer[Refe object SequenceDataset { + /** + * Hadoop configuration path to specify line width at + * which to hard wrap FASTA formatted sequences. Defaults to 60. + */ + val FASTA_LINE_WIDTH = "org.bdgenomics.adam.rdd.sequence.SequenceDataset.lineWidth" + /** * A genomic dataset that wraps a dataset of Sequence data. *