# HG changeset patch
# User ntino-krampis
# Date 1390610103 18000
# Node ID c81aa7ffced2f5a48e5320c078a84c8d491de94e
# Parent  beaf42837914648feb7826b1b40c7a303cb65dab
Deleted selected files

diff -r beaf42837914 -r c81aa7ffced2 viral_assembly_annotation/VIGOR.py
--- a/viral_assembly_annotation/VIGOR.py	Thu Jan 31 13:41:35 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Runs VIGOR3 on given input fasta file.
-"""
-
-import os, sys, subprocess, tempfile, shutil
-
-def __main__():
-	# Parse the command line options
-	(inputFasta,outputALN,outputCDS,outputFS,outputPEP,outputRPT,outputSTATS,outputTBL) = sys.argv[1:]
-	
-	# Set up output variables
-	outputDir = "/usr/local/VIGOR/tools/vigor/test"
-	outputName = "output"
-	outputLog = "%s/%s_log.txt"      % (outputDir,outputName)
-	vigorOutputALN = "%s/%s.aln"     % (outputDir,outputName)
-	vigorOutputCDS = "%s/%s.cds"     % (outputDir,outputName)
-	vigorOutputFS = "%s/%s.fs"       % (outputDir,outputName)
-	vigorOutputPEP = "%s/%s.pep"     % (outputDir,outputName)
-	vigorOutputRPT = "%s/%s.rpt"     % (outputDir,outputName)
-	vigorOutputSTATS = "%s/%s.stats" % (outputDir,outputName)
-	vigorOutputTBL = "%s/%s.tbl"     % (outputDir,outputName)
-	
-	# Create empty output log file (cannot be created by VIGOR command alone).
-	os.system("sudo touch %s" % outputLog)
-	os.system("sudo chmod 777 %s" % outputLog)
-	
-	# Run command
-	command = "/usr/local/VIGOR/tools/vigor/prod3/VIGOR3.pl -A -i %s -O %s/%s > %s" % (inputFasta,outputDir,outputName,outputLog)
-	os.system("sudo %s" % command)
-	os.system("sudo chmod 777 %s/%s.*" % (outputDir,outputName))
-	os.system("sudo cp %s %s" % (vigorOutputALN,outputALN))
-	os.system("sudo cp %s %s" % (vigorOutputCDS,outputCDS))
-	os.system("sudo cp %s %s" % (vigorOutputFS,outputFS))
-	os.system("sudo cp %s %s" % (vigorOutputPEP,outputPEP))
-	os.system("sudo cp %s %s" % (vigorOutputRPT,outputRPT))
-	os.system("sudo cp %s %s" % (vigorOutputSTATS,outputSTATS))
-	os.system("sudo cp %s %s" % (vigorOutputTBL,outputTBL))
-
-if __name__=="__main__": 
-	__main__()
diff -r beaf42837914 -r c81aa7ffced2 viral_assembly_annotation/VIGOR.xml
--- a/viral_assembly_annotation/VIGOR.xml	Thu Jan 31 13:41:35 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<tool id="VIGOR" name="VIGOR" version="1.0.0">
-	<description>Run VIGOR</description>
-	<command interpreter="python">
-		VIGOR.py $input $outputALN $outputCDS $outputFS $outputPEP $outputRPT $outputSTATS $outputTBL
-	</command>
-	<inputs>
-		<param name="input" label="Input FASTA" type="data" format="fasta" />
-	</inputs>
-	<outputs>
-		<data format="txt" name="outputALN" label="ALN from ${tool.name} on ${on_string}" />
-		<data format="fasta" name="outputCDS" label="CDS from ${tool.name} on ${on_string}" />
-		<data format="txt" name="outputFS" label="FS from ${tool.name} on ${on_string}" />
-		<data format="fasta" name="outputPEP" label="PEP from ${tool.name} on ${on_string}" />
-		<data format="txt" name="outputRPT" label="RPT from ${tool.name} on ${on_string}" />
-		<data format="txt" name="outputSTATS" label="STATS from ${tool.name} on ${on_string}" />
-		<data format="txt" name="outputTBL" label="TBL from ${tool.name} on ${on_string}" />
-	</outputs>
-	
-	<help>
-**What it does**
-
-This tool runs VIGOR on the input set of fasta sequences.
-	</help>
-</tool>
diff -r beaf42837914 -r c81aa7ffced2 viral_assembly_annotation/viral_assembly.py
--- a/viral_assembly_annotation/viral_assembly.py	Thu Jan 31 13:41:35 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Takes input from viral_assembly.xml and sends it to vir-assembly-pipeline.sh.
-"""
-
-import os, sys, subprocess, tempfile, shutil
-
-def __prepare_input__(draftFilename,finalFilename,finalDir):
-	result = "%s/%s" % (finalDir,finalFilename)
-	
-	if draftFilename == "None":
-		os.system("sudo touch %s" % result)
-	else:
-		os.system("sudo cp %s %s" % (draftFilename,result))
-	
-	return result
-
-def __main__():
-	# Parse the command line options
-	(input_454,input_Sanger,input_Solexa,input_Solexa_tp,database,outputFasta) = sys.argv[1:]
-	
-	# Copy the input files to the VHTNGS location. If an input file was not given, create an empty dummy file as a replacement.
-	inputDir = "/usr/local/VHTNGS"
-	
-	input_454_ready = __prepare_input__(input_454,"input_454.sff",inputDir)
-	input_Sanger_ready = __prepare_input__(input_Sanger,"input_Sanger.fasta",inputDir)
-	input_Solexa_ready = __prepare_input__(input_Solexa,"input_Solexa.fastq",inputDir)
-	input_Solexa_tp_ready = __prepare_input__(input_Solexa_tp,"input_Solexa.fastq.trimpoints",inputDir)
-	
-	command = "/usr/local/VHTNGS/vir-assembly-pipeline.sh %s %s %s %s %s" % (input_454_ready,input_Sanger_ready,input_Solexa_ready,input_Solexa_tp_ready,database)
-	virAssemblyOutput = "/usr/local/VHTNGS/project/mapping/sample_hybrid_edited_refs_consensus.fasta"
-	os.system("sudo %s" % command)
-	os.system("sudo chmod 777 %s" % virAssemblyOutput)
-	os.system("sudo cp %s %s" % (virAssemblyOutput,outputFasta))
-
-if __name__=="__main__": 
-  __main__()
diff -r beaf42837914 -r c81aa7ffced2 viral_assembly_annotation/viral_assembly.xml
--- a/viral_assembly_annotation/viral_assembly.xml	Thu Jan 31 13:41:35 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<tool id="vir_assembly" name="Viral Assembly" version="1.0.0">
-  <description>Run Viral assembly</description>
-  <command interpreter="python">
-    viral_assembly.py $input_454 $input_Sanger $input_Solexa $input_Solexa_tp $database $output_Fasta
-  </command>
-  <inputs>
-    <param name="input_454" label="454 reads" type="data" format="sff" optional="true"/>
-	<param name="input_Sanger" label="Sanger reads" type="data" format="fasta" optional="true" />
-	<param name="input_Solexa" label="Solexa reads" type="data" format="fastq" optional="true"/>
-	<param name="input_Solexa_tp" label="Solexa trimpoints" type="data" format="tabular" optional="true"/>
-    <param name="database" label="Viral database" type="select">
-	  <option value="barda">barda</option>
-	  <option value="giv">giv</option>
-	  <option value="giv3">giv3</option>
-	  <option value="piv">piv</option>
-	  <option value="swiv">swiv</option>
-	  <option value="rtv">rtv</option>
-	  <option value="gcv">gcv</option>
-	  <option value="veev">veev</option>
-	  <option value="hadv">hadv</option>
-	  <option value="mpv">mpv</option>
-	  <option value="norv">norv</option>
-	  <option value="vzv">vzv</option>
-	  <option value="rsv">rsv</option>
-	  <option value="jev">jev</option>
-	  <option value="yfv">yfv</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="fasta" name="output_Fasta" label="${tool.name} on ${on_string}" />
-  </outputs>
-  <help>
-
-**What it does**
-
-This tool uses vir-assembly-pipeline.sh to run viral assembly and consensus sequence generation on the input sequence data.
-  </help>
-</tool>