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changeset 0:3d22562b4489 draft

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Uploaded
author urgi-team
date Fri, 29 Apr 2016 09:11:18 -0400
parents
children 15d6811e6bf5
files TEiso/ClosestToStartSite_Wrapper.py TEiso/ClosestToStartSite_Wrapper.xml TEiso/CufflinksGTFToBed_Wrapper.py TEiso/CufflinksGTFToBed_Wrapper.xml TEiso/GFFToBed_Wrapper.py TEiso/GFFToBed_Wrapper.xml TEiso/tool_dependencies.xml
diffstat 7 files changed, 461 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/ClosestToStartSite_Wrapper.py	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+
+
+class ClosestToStartSiteWrapper(object):
+
+    def __init__(self):
+        self._options = None
+        
+        
+    def stop_err(self, msg ):
+        sys.stderr.write( "%s\n" % msg )
+        sys.exit()
+        
+        
+    def setAttributesFromCmdLine(self):
+        self._toolVersion = "1.0"
+        description = "ClosestToStartSite version %s" % self._toolVersion
+        epilog = "\n parses a bed file and create a bed file to create a report about positions of features A to features B. \n"
+        epilog += "example: ClosestToStartSite.py -i <inputFile> -o  <outputFile>\n"
+        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GTF File name(transcript.gtf of Cufflinks).",  default = "")
+        parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "Verbosity [optional] [default: 3]",default = 3)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+    def run(self):
+        prg = "ClosestToStartSite.py"
+        args = ""
+        args += "-i %s" % self._options.inputFile
+        cmd = "%s %s" %(prg, args)
+        print cmd
+        
+        try:
+            tmp_err = tempfile.NamedTemporaryFile().name
+            tmp_stderr = open( tmp_err, 'wb' )
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp_err, 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if stderr:
+                raise Exception, stderr
+        except Exception, e:
+            self.stop_err( 'Error in ClosestToStartSite:\n' + str( e ) ) 
+        
+if __name__ == "__main__":
+    iWrapper = ClosestToStartSiteWrapper()
+    iWrapper.setAttributesFromCmdLine()
+    iWrapper.run()    
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/ClosestToStartSite_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,133 @@
+<tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
+    <description>ClosestToStartSite parses a bed file and create a bed file to create a report about positions of features A to features B.</description>
+    <requirements>
+        <requirement type="package" version="1.0">TEiso_Tools</requirement>
+    </requirements>
+    <version_command>
+   ClosestToStartSite.py --version
+    </version_command>
+    <command interpreter="python">
+    ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+      
+**ClosestToStartSite_wrapper parses a bed file and create a bed file to create a report about positions of features A to features B.**
+
+
+**what it does :**
+
+parses a bed file and create a bed file to create a report about positions of features A to features B
+
+-----
+
+**input format :**
+
+.. class:: infomark
+
+**output format :**
+
+fake	140	532	CUFF.1.1	CUFF.1	+	26875.607
+
+-----
+
+
+
+******  "B_close_TSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+					              F[1]   gene             F[2]
+                                    =========================>
+                     ------------
+                    F[8]        F[9]
+    
+    
+                                   F[1]                     F[2]
+                                    <=========================
+                                                                ---------------
+
+
+******  "B_overlap_TSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            
+                                    F[1]   gene             F[2]
+                                    =========================>
+                             -------------
+                            F[8]        F[9]
+            
+                                                     gene
+                 					F[1]=========================>F[2]
+            
+      								F[8]---------------F[9]
+            
+               
+            
+                                   F[1]=============================>F[2]
+                F[8]---------------F[9]
+            
+            
+                                    F[1]<=============================F[2]
+                                                       ---------------------------
+                                                    F[8]           F[9]
+            
+            
+                                F[1]<=============================F[2]
+                                               F[8]---------------F[9]
+            
+                  
+                                                            F[1]<=============================F[2]
+                                                                                            F[8]---------------F[9]
+
+******  "B-inclus-A"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            
+                    
+            
+                                    F[1]            gene          F[2]
+                                    ==============================
+                                            -------------
+                                            F[8]        F[9]
+            
+******  "A-inclus-B"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            
+            
+                        
+                                    F[1]======================F[2]
+                    F[8]----------------------------------------------------F[9]
+            
+            
+            
+            
+         					         F[1]==================================>F[2]
+             F[8]----------------------------------------------------------F[9]
+             
+             
+             
+                 					F[1]<==================================F[2]
+                    F[8]----------------------------------------------------------F[9]
+             
+             
+            
+******  "A-inclus-B-inTSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~           
+                    
+ 											 F[1]<==================================F[2]
+                       [8]----------------------------------------------------------F[9]
+            
+                  
+ 												F[1]==================================>F[2]
+                                   					F[8]----------------------------------------------------------F[9]
+            
+    
+-----
+
+**reference :**
+
+]]>
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/CufflinksGTFToBed_Wrapper.py	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+
+
+class CufflinksGTFToBedWrapper(object):
+
+    def __init__(self):
+        self._options = None
+        
+        
+    def stop_err(self, msg ):
+        sys.stderr.write( "%s\n" % msg )
+        sys.exit()
+        
+        
+    def setAttributesFromCmdLine(self):
+        self._toolVersion = "1.0"
+        description = "CufflinksGTFToBed version %s" % self._toolVersion
+        epilog = "\n parses a GTF file of Cufflinks and create a bed file. \n"
+        epilog += "example: CufflinksGTFToBed.py -i <inputFile> -o  <outputFile>\n"
+        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GTF File name(transcript.gtf of Cufflinks).",  default = "")
+        parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "Verbosity [optional] [default: 3]",default = 3)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+    def run(self):
+        prg = "CufflinksGTFToBed.py"
+        args = ""
+        args += "-i %s" % self._options.inputFile
+        cmd = "%s %s" %(prg, args)
+        print cmd
+        
+        try:
+            tmp_err = tempfile.NamedTemporaryFile().name
+            tmp_stderr = open( tmp_err, 'wb' )
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp_err, 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if stderr:
+                raise Exception, stderr
+        except Exception, e:
+            self.stop_err( 'Error in TranscriptToBed:\n' + str( e ) ) 
+        
+if __name__ == "__main__":
+    iWrapper = CufflinksGTFToBedWrapper()
+    iWrapper.setAttributesFromCmdLine()
+    iWrapper.run()    
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/CufflinksGTFToBed_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,52 @@
+<tool id="CufflinksGTFToBed" name="CufflinksGTFToBed" version="1.0">
+    <description>CufflinksGTFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
+    <requirements>
+        <requirement type="package" version="1.0">TEiso_Tools</requirement>
+    </requirements>
+    <version_command>
+   CufflinksGTFToBed.py --version
+    </version_command>
+    <command interpreter="python">
+    CufflinksGTFToBed_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="gtf" label="indicate a transcript GTF file of cufflinks."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+      
+**CufflinksGTFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
+
+
+**what it does :**
+
+converts a result GTF file of Cufflinks into a bed file. 
+
+It can take: Chromosome, Start, End, strand, Isoform ID, Gene ID, value of FPKM
+
+-----
+
+**input format :**
+
+.. class:: infomark
+
+fake	Cufflinks	transcript	140	532	1000	+	.	gene_id "CUFF.1"; 
+transcript_id "CUFF.1.1"; FPKM "26875.6073354154"; frac "1.000000"; conf_lo "24989.806681"; conf_hi "28761.407990"; cov "752.375132";
+-----
+
+**output format :**
+
+fake	140	532	CUFF.1.1	CUFF.1	+	26875.607
+
+-----
+
+
+-----
+
+**reference :**
+
+]]>
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/GFFToBed_Wrapper.py	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+
+
+class GFFToBedWrapper(object):
+
+    def __init__(self):
+        self._options = None
+        
+        
+    def stop_err(self, msg ):
+        sys.stderr.write( "%s\n" % msg )
+        sys.exit()
+        
+        
+    def setAttributesFromCmdLine(self):
+        self._toolVersion = "1.0"
+        description = "GFFToBed version %s" % self._toolVersion
+        epilog = "\n parses a GFF file and create a bed file. \n"
+        epilog += "example: GFFToBed.py -i <inputFile> -o  <outputFile>\n"
+        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GFF File name.",  default = "")
+        parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "Verbosity [optional] [default: 3]",default = 3)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+    def run(self):
+        prg = "GFFToBed.py"
+        args = ""
+        args += "-i %s" % self._options.inputFile
+        cmd = "%s %s" %(prg, args)
+        print cmd
+        
+        try:
+            tmp_err = tempfile.NamedTemporaryFile().name
+            tmp_stderr = open( tmp_err, 'wb' )
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp_err, 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if stderr:
+                raise Exception, stderr
+        except Exception, e:
+            self.stop_err( 'Error in GFFToBed:\n' + str( e ) ) 
+        
+if __name__ == "__main__":
+    iWrapper = GFFToBedWrapper()
+    iWrapper.setAttributesFromCmdLine()
+    iWrapper.run()    
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/GFFToBed_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,53 @@
+<tool id="GFFToBed" name="GFFToBed" version="1.0">
+    <description>GFFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
+    <requirements>
+        <requirement type="package" version="1.0">TEiso_Tools</requirement>
+    </requirements>
+    <version_command>
+   GFFToBed.py --version
+    </version_command>
+    <command interpreter="python">
+    GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+      
+**GFFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
+
+
+**what it does :**
+
+converts a result GTF file of Cufflinks into a bed file. 
+
+It can take: Chromosome, Start, End, ID, Target, strand
+
+-----
+
+**input format :**
+
+.. class:: infomark
+
+2L	DmelCaf1_2_2_REPET_TEs	match	47519	52563	0.0	+	.	ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8
+
+
+-----
+
+**output format :**
+
+2L	47519	52563	ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11		RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050		+
+
+-----
+
+
+-----
+
+**reference :**
+
+]]>
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/tool_dependencies.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="TEiso_Tools" version="1.0">
+		<install version="1.0">
+			<actions>
+				<action type="download_by_url">https://urgi.versailles.inra.fr/download/TEiso/TEisotools-1.0.tar.gz</action>
+				<action type="shell_command">python setup_TEiso.py install</action>
+				<action type="move_directory_files">
+					<source_directory>.</source_directory>
+					<destination_directory>$INSTALL_DIR</destination_directory>
+				</action>
+				<action type="set_environment">
+					<environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+	</package>
+</tool_dependency>