# 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 @@
-
- Run VIGOR
-
- VIGOR.py $input $outputALN $outputCDS $outputFS $outputPEP $outputRPT $outputSTATS $outputTBL
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-**What it does**
-
-This tool runs VIGOR on the input set of fasta sequences.
-
-
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 @@
-
- Run Viral assembly
-
- viral_assembly.py $input_454 $input_Sanger $input_Solexa $input_Solexa_tp $database $output_Fasta
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-**What it does**
-
-This tool uses vir-assembly-pipeline.sh to run viral assembly and consensus sequence generation on the input sequence data.
-
-