From 32d55edd2b35dabf2d4fcff421e55cb274665427 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 29 Jan 2015 17:02:11 +0100
Subject: [PATCH] Remove old sync script and its wrapper
---
.idea/misc.xml | 3 +
.../biopet/scripts/sync_paired_end_reads.py | 126 ------------------
.../lumc/sasc/biopet/scripts/FastqSync.scala | 116 ----------------
3 files changed, 3 insertions(+), 242 deletions(-)
delete mode 100644 public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
delete mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala
diff --git a/.idea/misc.xml b/.idea/misc.xml
index e10c5f30b..59f0fb2d0 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -1,5 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
+ <component name="EntryPointsManager">
+ <entry_points version="2.0" />
+ </component>
<component name="MavenProjectsManager">
<option name="originalFiles">
<list>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
deleted file mode 100644
index be4ab0035..000000000
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/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.
-#
-
-"""
-(Re-)sync two filtered paired end FASTQ files.
-
-Given two filtered paired end read files and one of the original read files,
-re-sync the filtered reads by filtering out anything that is only present in
-one of the two files.
-
-Usage:
- {command} <orig.fq> <reads_1.fq> <reads_2.fq> \\
- <reads_1.synced.fq> <reads_2.synced.fq>
-
-The synced reads are written to disk as <reads_1.synced.fq> and
-<reads_2.synced.fq>. Afterwards some counts are printed.
-
-
-Both Illumina old-style and new-style paired-end header lines are supported.
-
-The original read file is used to speed up processing: it contains all
-possible reads from both edited reads (in all files in the same order) so it
-can process all files line by line, not having to read a single file in
-memory. Some ideas were taken from [1].
-
-[1] https://gist.github.com/588841/
-
-2011-11-03, Martijn Vermaat <m.vermaat.hg@lumc.nl>
-"""
-
-
-import sys
-import re
-
-
-def sync_paired_end_reads(original, reads_a, reads_b, synced_a, synced_b):
- """
- Filter out reads from two paired end read files that are not present in
- both of them. Do this in a reasonable amount of time by using a file
- containing all of the reads for one of the paired ends.
-
- All arguments are open file handles.
-
- @arg original: File containing all original reads for one of the paired
- ends.
- @arg reads_a: First from paired end read files.
- @arg reads_b: Second from paired end read files.
- @arg synced_a: Filtered reads from first paired end read file.
- @arg synced_b: Filtered reads from second paired end read file.
-
- @return: Triple (filtered_a, filtered_b, kept) containing counts
- of the number of reads filtered from both input files and
- the total number of reads kept in the synced results.
-
- @todo: Print warnings if obvious things are not right (a or b still has
- lines after original is processed).
- """
- # This matches 1, 2, or 3 preceded by / _ or whitespace. Its rightmost
- # match in a header line is used to identify the read pair.
- sep = re.compile('[\s_/][123]')
-
- def next_record(fh):
- return [fh.readline().strip() for i in range(4)]
-
- def head(record):
- return sep.split(record[0])[:-1]
-
- headers = (sep.split(x.strip())[:-1] for i, x in enumerate(original)
- if not (i % 4))
-
- filtered_a = filtered_b = kept = 0
-
- a, b = next_record(reads_a), next_record(reads_b)
-
- for header in headers:
- if header == head(a) and head(b) != header:
- a = next_record(reads_a)
- filtered_a += 1
-
- if header == head(b) and head(a) != header:
- b = next_record(reads_b)
- filtered_b += 1
-
- if header == head(a) == head(b):
- print >>synced_a, '\n'.join(a)
- print >>synced_b, '\n'.join(b)
- a, b = next_record(reads_a), next_record(reads_b)
- kept += 1
-
- return filtered_a, filtered_b, kept
-
-
-if __name__ == '__main__':
- if len(sys.argv) < 6:
- sys.stderr.write(__doc__.split('\n\n\n')[0].strip().format(
- command=sys.argv[0]) + '\n')
- sys.exit(1)
- try:
- original = open(sys.argv[1], 'r')
- reads_a = open(sys.argv[2], 'r')
- reads_b = open(sys.argv[3], 'r')
- synced_a = open(sys.argv[4], 'w')
- synced_b = open(sys.argv[5], 'w')
- filtered_a, filtered_b, kept = \
- sync_paired_end_reads(original, reads_a, reads_b,
- synced_a, synced_b)
- print 'Filtered %i reads from first read file.' % filtered_a
- print 'Filtered %i reads from second read file.' % filtered_b
- print 'Synced read files contain %i reads.' % kept
- except IOError as (_, message):
- sys.stderr.write('Error: %s\n' % message)
- sys.exit(1)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala
deleted file mode 100644
index 6cada2301..000000000
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala
+++ /dev/null
@@ -1,116 +0,0 @@
-/**
- * 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 java.io.File
-
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-
-import argonaut._, Argonaut._
-import scalaz._, Scalaz._
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
-
-import scala.io.Source
-
-class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
- setPythonScript("sync_paired_end_reads.py")
-
- @Input(doc = "Start fastq")
- var input_start_fastq: File = _
-
- @Input(doc = "R1 input")
- var input_R1: File = _
-
- @Input(doc = "R2 input")
- var input_R2: File = _
-
- @Output(doc = "R1 output")
- var output_R1: File = _
-
- @Output(doc = "R2 output")
- var output_R2: File = _
-
- //No output Annotation so file
- var output_stats: File = _
-
- def cmdLine = {
- getPythonCommand +
- required(input_start_fastq) +
- required(input_R1) +
- required(input_R2) +
- required(output_R1) +
- required(output_R2) +
- " > " +
- required(output_stats)
- }
-
- def getSummary: Json = {
- val R1_filteredR = """Filtered (\d*) reads from first read file.""".r
- val R2_filteredR = """Filtered (\d*) reads from second read file.""".r
- val readsLeftR = """Synced read files contain (\d*) reads.""".r
-
- var R1_filtered = 0
- var R2_filtered = 0
- var readsLeft = 0
-
- if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
- line match {
- case R1_filteredR(m) => R1_filtered = m.toInt
- case R2_filteredR(m) => R2_filtered = m.toInt
- case readsLeftR(m) => readsLeft = m.toInt
- case _ =>
- }
- }
-
- return ("num_reads_discarded_R1" := R1_filtered) ->:
- ("num_reads_discarded_R2" := R2_filtered) ->:
- ("num_reads_kept" := readsLeft) ->:
- jEmptyObject
- }
-}
-
-object FastqSync {
- def apply(root: Configurable, input_start_fastq: File, input_R1: File, input_R2: File,
- output_R1: File, output_R2: File, output_stats: File): FastqSync = {
- val fastqSync = new FastqSync(root)
- fastqSync.input_start_fastq = input_start_fastq
- fastqSync.input_R1 = input_R1
- fastqSync.input_R2 = input_R2
- fastqSync.output_R1 = output_R1
- fastqSync.output_R2 = output_R2
- fastqSync.output_stats = output_stats
- return fastqSync
- }
-
- def mergeSummaries(jsons: List[Json]): Json = {
- var R1_filtered = 0
- var R2_filtered = 0
- var readsLeft = 0
-
- for (json <- jsons) {
- R1_filtered += json.field("num_reads_discarded_R1").get.numberOrZero.toInt
- R2_filtered += json.field("num_reads_discarded_R2").get.numberOrZero.toInt
- readsLeft += json.field("num_reads_kept").get.numberOrZero.toInt
- }
-
- return ("num_reads_discarded_R1" := R1_filtered) ->:
- ("num_reads_discarded_R2" := R2_filtered) ->:
- ("num_reads_kept" := readsLeft) ->:
- jEmptyObject
- }
-}
\ No newline at end of file
--
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