Remove old scripts

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/prefixFastq.py

-#!/usr/bin/env python
-#
-# Biopet is built on top of GATK Queue for building bioinformatic
-# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-# should also be able to execute Biopet tools and pipelines.
-#
-# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-#
-# Contact us at: sasc@lumc.nl
-#
-# A dual licensing mode is applied. The source code within this project that are
-# not part of GATK Queue is freely available for non-commercial use under an AGPL
-# license; For commercial users or users who do not want to follow the AGPL
-# license, please contact us to obtain a separate license.
-#
-
-
-# prep_deepsage.py
-#
-# Script for preprocessing deepSAGE sequencing samples.
-#
-# Adapted from: http://galaxy.nbic.nl/u/pacthoen/w/deepsagelumc
-
-import argparse
-
-from Bio import SeqIO
-
-PREFIX = 'CATG'
-
-def prep_deepsage(input_fastq, output_fastq, is_gzip, seq):
-    if is_gzip:
-        import gzip
-        opener = gzip.GzipFile
-    else:
-        opener = open
-    with opener(input_fastq, 'r') as in_handle, open(output_fastq, 'w') as \
-            out_handle:
-        # adapted from fastools.fastools.add
-        # not importing since we also need to cut away parts of the sequence
-        for rec in SeqIO.parse(in_handle, 'fastq'):
-            qual = rec.letter_annotations['phred_quality']
-            rec.letter_annotations = {}
-            rec.seq = seq + rec.seq
-            rec.letter_annotations = {'phred_quality': [40] * len(seq) +
-                    qual}
-            SeqIO.write(rec, out_handle, "fastq")
-
-
-if __name__ == '__main__':
-
-    parser = argparse.ArgumentParser()
-    parser.add_argument('input_fastq', type=str,
-            help="Path to input FASTQ file")
-    parser.add_argument('-o', '--output', type=str,
-            dest='output_fastq',
-            default="prep_deepsage_output.fq",
-            help="Path to output FASTQ file")
-    parser.add_argument('--gzip', dest='gzip',
-            action='store_true',
-            help="Whether input FASTQ file is gzipped or not.")
-    parser.add_argument('--prefix', dest='prefix', type=str,
-            default=PREFIX,
-            help="Whether input FASTQ file is gzipped or not.")
-
-    args = parser.parse_args()
-
-    prep_deepsage(args.input_fastq, args.output_fastq, args.gzip, args.prefix)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/prefixFastq.scala

-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.scripts
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-import java.io.File
-
-class PrefixFastq(val root: Configurable) extends PythonCommandLineFunction {
-  setPythonScript("prefixFastq.py")
-
-  @Input(doc = "Input file")
-  var input: File = _
-
-  @Output(doc = "output File")
-  var output: File = _
-
-  @Argument(doc = "Prefix sequence")
-  var prefix: String = "CATG"
-
-  @Argument(doc = "Input file is gziped", required = false)
-  var gzip: Boolean = _
-
-  override def beforeCmd {
-    if (input.getName.endsWith(".gzip") || input.getName.endsWith("gz")) gzip = true
-  }
-
-  def cmdLine = getPythonCommand +
-    required("-o", output) +
-    required("--prefix", prefix) +
-    required(input)
-}
-
-object PrefixFastq {
-  def apply(root: Configurable, input: File, outputDir: String): PrefixFastq = {
-    val prefixFastq = new PrefixFastq(root)
-    prefixFastq.input = input
-    prefixFastq.output = new File(outputDir, input.getName + ".prefix.fastq")
-    return prefixFastq
-  }
-}