From a7522c766ccb8ed74f1fa56a872e9c3e5eeec240 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 23 Jul 2014 18:32:00 +0200
Subject: [PATCH] Add initial wrapper for seqtk
---
.../nl/lumc/sasc/biopet/function/Seqtk.scala | 107 ++++++++++++++++++
1 file changed, 107 insertions(+)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
new file mode 100644
index 000000000..5cc3d8cab
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
@@ -0,0 +1,107 @@
+package nl.lumc.sasc.biopet.function
+
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+abstract class Seqtk extends BiopetCommandLineFunction {
+ executable = config("exe", default = "seqtk", submodule = "seqtk")
+ override def versionCommand = executable
+ override val versionRegex = """Version: (.*)""".r
+}
+
+class SeqtkSeq(val root: Configurable) extends Seqtk {
+ @Input(doc = "Input file (FASTQ or FASTA)")
+ var input: File = _
+
+ @Output(doc = "Output file")
+ var output: File = _
+
+ /* mask bases with quality lower than INT [0] */
+ var q: Option[Int] = config("q")
+
+ /* masked bases converted to CHAR; 0 for lowercase [0] */
+ var n: String = config("n")
+
+ /* number of residues per line; 0 for 2^32-1 [0] */
+ var l: Option[Int] = config("l")
+
+ /* quality shift: ASCII-INT gives base quality [33] */
+ var Q: Option[Int] = config("Q")
+
+ /* random seed (effective with -f) [11] */
+ var s: Option[Int] = config("s")
+
+ /* sample FLOAT fraction of sequences [1] */
+ var f: Option[Int] = config("f")
+
+ /* mask regions in BED or name list FILE [null] */
+ var M: File = config("M")
+
+ /* drop sequences with length shorter than INT [0] */
+ var L: Option[Int] = config("L")
+
+ /* mask complement region (effective with -M) */
+ var c: Boolean = config("c")
+
+ /* reverse complement */
+ var r: Boolean = config("r")
+
+ /* force FASTA output (discard quality) */
+ var A: Boolean = config("A")
+
+ /* drop comments at the header lines */
+ var C: Boolean = config("C")
+
+ /* drop sequences containing ambiguous bases */
+ var N: Boolean = config("N")
+
+ /* output the 2n-1 reads only */
+ var flag1: Boolean = config("1")
+
+ /* output the 2n reads only */
+ var flag2: Boolean = config("2")
+
+ /* shift quality by '(-Q) - 33' */
+ var V: Boolean = config("V")
+
+ def cmdLine = {
+ required(executable) +
+ " seq " +
+ optional("-q", q) +
+ optional("-n", n) +
+ optional("-l", l) +
+ optional("-Q", Q) +
+ optional("-s", s) +
+ optional("-f", f) +
+ optional("-M", M) +
+ optional("-L", L) +
+ conditional(c, "-c") +
+ conditional(r, "-r") +
+ conditional(A, "-A") +
+ conditional(C, "-C") +
+ conditional(N, "-N") +
+ conditional(flag1, "-1") +
+ conditional(flag2, "-2") +
+ conditional(V, "-V") +
+ required(input) +
+ " > " + required(output)
+ }
+
+ /**
+ * Calculates the offset required for the -Q flag for format conversion (-V flag set).
+ * This is required since seqtk computes the encoding offset indirectly from the input
+ * and output offsets.
+ *
+ * @param inQualOffset ASCII offset of the input file encoding
+ * @param outQualOffset ASCII offset of the output file encoding
+ * @return the value to be used with the -Q flag with -V set
+ */
+ def calcQForV(inQualOffset: Int, outQualOffset: Int): Int = {
+ // For the input for the -Q flag for seqtk, together with -V
+ inQualOffset - (outQualOffset - 33)
+ }
+}
--
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