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changeset 56:97aa2e42bfdf

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Uploaded
author m-zytnicki
date Wed, 05 Feb 2014 11:51:11 -0500
parents 2ac71607aa60
children 36eaa579fdb6
files SMART/Java/Python/__init__.pyc SMART/Java/Python/cleaning/CleanerChooser.pyc SMART/Java/Python/cleaning/DefaultCleaner.pyc SMART/Java/Python/cleaning/GffCleaner.py SMART/Java/Python/cleaning/GffCleaner.pyc SMART/Java/Python/cleaning/GtfCleaner.py SMART/Java/Python/cleaning/GtfCleaner.pyc SMART/Java/Python/cleaning/TranscriptListCleaner.pyc SMART/Java/Python/cleaning/__init__.pyc SMART/Java/Python/misc/Progress.pyc SMART/Java/Python/misc/UnlimitedProgress.pyc SMART/Java/Python/misc/Utils.pyc SMART/Java/Python/misc/__init__.pyc SMART/Java/Python/mySql/MySqlTable.pyc SMART/Java/Python/mySql/__init__.pyc SMART/Java/Python/ncList/FileSorter.pyc SMART/Java/Python/ncList/NCIndex.pyc SMART/Java/Python/ncList/NCList.pyc SMART/Java/Python/ncList/NCListCursor.pyc SMART/Java/Python/ncList/NCListFilePickle.pyc SMART/Java/Python/ncList/__init__.pyc SMART/Java/Python/structure/Bins.pyc SMART/Java/Python/structure/Interval.pyc SMART/Java/Python/structure/Mapping.pyc SMART/Java/Python/structure/Sequence.pyc SMART/Java/Python/structure/SequenceList.pyc SMART/Java/Python/structure/SubMapping.pyc SMART/Java/Python/structure/Transcript.pyc SMART/Java/Python/structure/TranscriptList.pyc SMART/Java/Python/structure/__init__.pyc SMART/Java/__init__.pyc SMART/__init__.pyc SMART/galaxy/Clusterize.xml SMART/galaxy/CollapseReads.xml SMART/galaxy/CompareOverlappingSmallQuery.xml SMART/galaxy/CompareOverlappingSmallRef.xml SMART/galaxy/ConvertTranscriptFile.xml SMART/galaxy/removeExonLines.xml SMART/galaxy/removeIntrons.xml commons/__init__.pyc commons/core/__init__.pyc commons/core/checker/RepetException.pyc commons/core/checker/__init__.pyc commons/core/coord/Align.pyc commons/core/coord/Map.pyc commons/core/coord/Range.pyc commons/core/coord/__init__.pyc commons/core/parsing/AxtParser.pyc commons/core/parsing/BamParser.pyc commons/core/parsing/BedParser.pyc commons/core/parsing/BlastParser.pyc commons/core/parsing/BowtieParser.pyc commons/core/parsing/CoordsParser.pyc commons/core/parsing/ElandParser.pyc commons/core/parsing/ExoParser.pyc commons/core/parsing/FastaParser.pyc commons/core/parsing/FastqParser.pyc commons/core/parsing/GffParser.pyc commons/core/parsing/GtfParser.pyc commons/core/parsing/MapParser.pyc commons/core/parsing/MapperParser.pyc commons/core/parsing/MaqParser.pyc commons/core/parsing/NCListParser.pyc commons/core/parsing/ParserChooser.pyc commons/core/parsing/PklParser.pyc commons/core/parsing/PslParser.pyc commons/core/parsing/RmapParser.pyc commons/core/parsing/SamParser.pyc commons/core/parsing/SeqmapParser.pyc commons/core/parsing/SequenceListParser.pyc commons/core/parsing/ShrimpParser.pyc commons/core/parsing/Soap2Parser.pyc commons/core/parsing/SoapParser.pyc commons/core/parsing/TranscriptListParser.pyc commons/core/parsing/WigParser.pyc commons/core/parsing/__init__.pyc commons/core/seq/Bioseq.pyc commons/core/seq/__init__.pyc commons/core/writer/BedWriter.pyc commons/core/writer/CsvWriter.pyc commons/core/writer/EmblWriter.pyc commons/core/writer/FastaWriter.pyc commons/core/writer/FastqWriter.pyc commons/core/writer/GbWriter.pyc commons/core/writer/Gff2Writer.pyc commons/core/writer/Gff3Writer.pyc commons/core/writer/GtfWriter.pyc commons/core/writer/MapWriter.pyc commons/core/writer/SamWriter.pyc commons/core/writer/SequenceListWriter.pyc commons/core/writer/TranscriptListWriter.pyc commons/core/writer/UcscWriter.pyc commons/core/writer/WigWriter.pyc commons/core/writer/WriterChooser.pyc commons/core/writer/__init__.pyc
diffstat 95 files changed, 88 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
Binary file SMART/Java/Python/__init__.pyc has changed
Binary file SMART/Java/Python/cleaning/CleanerChooser.pyc has changed
Binary file SMART/Java/Python/cleaning/DefaultCleaner.pyc has changed
--- a/SMART/Java/Python/cleaning/GffCleaner.py	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/Java/Python/cleaning/GffCleaner.py	Wed Feb 05 11:51:11 2014 -0500
@@ -123,7 +123,7 @@
 	def parse(self):
 		progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
 		for cpt, line in enumerate(self.inputHandle):
-			if not line or line[0] == "#": continue
+			if not line or (not line.strip()) or line[0] == "#": continue
 			if line[0] == ">": break
 			parsedLine = ParsedLine(line, cpt)
 			if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
Binary file SMART/Java/Python/cleaning/GffCleaner.pyc has changed
--- a/SMART/Java/Python/cleaning/GtfCleaner.py	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/Java/Python/cleaning/GtfCleaner.py	Wed Feb 05 11:51:11 2014 -0500
@@ -96,7 +96,7 @@
 	def parse(self):
 		progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
 		for cpt, line in enumerate(self.inputHandle):
-			if not line or line[0] == "#": continue
+			if not line or (not line.strip()) or line[0] == "#": continue
 			parsedLine = ParsedLine(line, cpt)
 			if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
 				transcriptId = parsedLine.transcriptId
Binary file SMART/Java/Python/cleaning/GtfCleaner.pyc has changed
Binary file SMART/Java/Python/cleaning/TranscriptListCleaner.pyc has changed
Binary file SMART/Java/Python/cleaning/__init__.pyc has changed
Binary file SMART/Java/Python/misc/Progress.pyc has changed
Binary file SMART/Java/Python/misc/UnlimitedProgress.pyc has changed
Binary file SMART/Java/Python/misc/Utils.pyc has changed
Binary file SMART/Java/Python/misc/__init__.pyc has changed
Binary file SMART/Java/Python/mySql/MySqlTable.pyc has changed
Binary file SMART/Java/Python/mySql/__init__.pyc has changed
Binary file SMART/Java/Python/ncList/FileSorter.pyc has changed
Binary file SMART/Java/Python/ncList/NCIndex.pyc has changed
Binary file SMART/Java/Python/ncList/NCList.pyc has changed
Binary file SMART/Java/Python/ncList/NCListCursor.pyc has changed
Binary file SMART/Java/Python/ncList/NCListFilePickle.pyc has changed
Binary file SMART/Java/Python/ncList/__init__.pyc has changed
Binary file SMART/Java/Python/structure/Bins.pyc has changed
Binary file SMART/Java/Python/structure/Interval.pyc has changed
Binary file SMART/Java/Python/structure/Mapping.pyc has changed
Binary file SMART/Java/Python/structure/Sequence.pyc has changed
Binary file SMART/Java/Python/structure/SequenceList.pyc has changed
Binary file SMART/Java/Python/structure/SubMapping.pyc has changed
Binary file SMART/Java/Python/structure/Transcript.pyc has changed
Binary file SMART/Java/Python/structure/TranscriptList.pyc has changed
Binary file SMART/Java/Python/structure/__init__.pyc has changed
Binary file SMART/Java/__init__.pyc has changed
Binary file SMART/__init__.pyc has changed
--- a/SMART/galaxy/Clusterize.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/Clusterize.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -15,6 +15,8 @@
 			-f gff3
 		#elif $formatType.FormatInputFileName == 'sam':
 			-f sam
+		#elif $formatType.FormatInputFileName == 'bam':
+			-f bam
 		#elif $formatType.FormatInputFileName == 'gtf':
 			-f gtf
 		#end if
@@ -32,6 +34,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -49,6 +52,9 @@
 			<when value="sam">
 				<param name="inputFileName" format="sam" type="data" label="Input File"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName" format="bam" type="data" label="Input File"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
 			</when>
--- a/SMART/galaxy/CollapseReads.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CollapseReads.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -15,6 +15,8 @@
 			-f gff3
 		#elif $formatType.FormatInputFileName == 'sam':
 			-f sam
+		#elif $formatType.FormatInputFileName == 'bam':
+			-f bam
 		#elif $formatType.FormatInputFileName == 'gtf':
 			-f gtf
 		#end if
@@ -30,6 +32,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -47,6 +50,9 @@
 			<when value="sam">
 				<param name="inputFileName" format="sam" type="data" label="Input File"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName" format="bam" type="data" label="Input File"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
 			</when>
--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -15,6 +15,8 @@
 			-f gff3
 		#elif $formatType.FormatInputFileName1 == 'sam':
 			-f sam
+		#elif $formatType.FormatInputFileName1 == 'bam':
+			-f bam
 		#elif $formatType.FormatInputFileName1 == 'gtf':
 			-f gtf
 		#end if
@@ -29,6 +31,8 @@
 			-g gff3
 		#elif $formatType2.FormatInputFileName2 == 'sam':
 			-g sam
+		#elif $formatType2.FormatInputFileName2 == 'bam':
+			-g bam
 		#elif $formatType2.FormatInputFileName2 == 'gtf':
 		    -g gtf
 		#end if
@@ -64,6 +68,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -81,6 +86,9 @@
 			<when value="sam">
 				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
 								                        </when>
@@ -93,6 +101,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -110,6 +119,9 @@
 			<when value="sam">
 				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
 			</when>
--- a/SMART/galaxy/CompareOverlappingSmallRef.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallRef.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -15,6 +15,8 @@
 			-f gff3
 		#elif $formatType.FormatInputFileName1 == 'sam':
 			-f sam
+		#elif $formatType.FormatInputFileName1 == 'bam':
+			-f bam
 		#elif $formatType.FormatInputFileName1 == 'gtf':
 			-f gtf
 		#end if
@@ -29,6 +31,8 @@
 			-g gff3
 		#elif $formatType2.FormatInputFileName2 == 'sam':
 			-g sam
+		#elif $formatType2.FormatInputFileName2 == 'bam':
+			-g bam
 		#elif $formatType2.FormatInputFileName2 == 'gtf':
 		    -g gtf
 		#end if
@@ -64,6 +68,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -81,6 +86,9 @@
 			<when value="sam">
 				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
 								                        </when>
@@ -93,6 +101,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -110,6 +119,9 @@
 			<when value="sam">
 				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
 			</when>
--- a/SMART/galaxy/ConvertTranscriptFile.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/ConvertTranscriptFile.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -3,33 +3,14 @@
 	<requirements>
 		<requirement type="set_environment">PYTHONPATH</requirement>
 	</requirements>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName 
-	  #if $inputFormatType.FormatInputFileName == 'gff3':
-	  	-f gff3
-	  #elif $inputFormatType.FormatInputFileName == 'bed': 
-	 	-f bed 
-	  #elif $inputFormatType.FormatInputFileName == 'bam': 
-	 	-f blast
-	  #elif $inputFormatType.FormatInputFileName == 'sam': 
-	 	-f sam
-	  #elif $inputFormatType.FormatInputFileName == 'gtf': 
-	 	-f gtf
-          #end if
-	  
-	 -g $outputFormatType.outFormat
-	  
-	  -n $name
-	  $strand
-	  -o $outputFile
-	 
-  </command>
+  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile </command>
   <inputs>
 	  <conditional name="inputFormatType">
 		  <param name="FormatInputFileName"  type="select" label="Input File Format">
 			  <option value="gff3">GFF3</option> 
 			  <option value="bed">BED</option> 
+			  <option value="sam">SAM</option> 
 			  <option value="bam">BAM</option> 
-			  <option value="sam">SAM</option> 
 			  <option value="gtf">GTF</option> 
 		  </param>
 		  <when value="gff3">  
@@ -38,12 +19,12 @@
 		  <when value="bed">  
 			  <param name="inputFileName" format="bed" type="data" label="Input File"/>
 		  </when>
+		  <when value="sam">  
+			  <param name="inputFileName" format="sam" type="data" label="Input File"/>
+		  </when>
 		  <when value="bam">  
 			  <param name="inputFileName" format="bam" type="data" label="Input File"/>
 		  </when>
-		  <when value="sam">  
-			  <param name="inputFileName" format="sam" type="data" label="Input File"/>
-		  </when>
 		  <when value="gtf">  
 			  <param name="inputFileName" format="gtf" type="data" label="Input File"/>
 		  </when>
--- a/SMART/galaxy/removeExonLines.xml	Fri Jan 10 08:59:23 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<tool id="removeExonLines" name="remove exon lines">
-  <description>Removes the lines containing Exon.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
-  <command interpreter="sh"> ../Java/Python/removeExonLines.sh $inputFile > $outputFile  </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[remove exon line] output file"/>
-  </outputs>
-
-  <help>
-	command example: sh removeExonLines.sh input.gff3
-  </help>
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/removeIntrons.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -0,0 +1,45 @@
+<tool id="removeIntrons" name="remove introns">
+  <description>Removes the introns of the transcript files.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+  <command interpreter="python"> ../Java/Python/RemoveExons.py -i $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile  </command>
+  <inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName1" type="select" label="query File Format">
+				<option value="bed">bed</option>
+				<option value="gff">gff</option>
+				<option value="gff2">gff2</option>
+				<option value="gff3">gff3</option>
+				<option value="sam">sam</option>
+				<option value="gtf">gtf</option>
+			</param>
+			<when value="bed">
+				<param name="inputFileName" format="bed" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName" format="gff" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File 1"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File 1"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File 1"/>
+			</when>
+		</conditional>
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[remove introns] output file"/>
+  </outputs>
+
+  <help>
+	Simply remove the introns of the input file, thus getting the unmatured transcript.
+  </help>
+</tool>
Binary file commons/__init__.pyc has changed
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