Previous changeset 55:2ac71607aa60 (2014-01-10) Next changeset 57:36eaa579fdb6 (2014-02-07) |
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Uploaded |
modified:
SMART/Java/Python/cleaning/GffCleaner.py SMART/Java/Python/cleaning/GtfCleaner.py SMART/galaxy/Clusterize.xml SMART/galaxy/CollapseReads.xml SMART/galaxy/CompareOverlappingSmallQuery.xml SMART/galaxy/CompareOverlappingSmallRef.xml SMART/galaxy/ConvertTranscriptFile.xml |
added:
SMART/Java/Python/__init__.pyc SMART/Java/Python/cleaning/CleanerChooser.pyc SMART/Java/Python/cleaning/DefaultCleaner.pyc SMART/Java/Python/cleaning/GffCleaner.pyc 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/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 |
removed:
SMART/galaxy/removeExonLines.xml |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/__init__.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/CleanerChooser.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/DefaultCleaner.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GffCleaner.py --- 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 |
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@@ -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: |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GffCleaner.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GtfCleaner.py --- 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 |
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@@ -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 |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GtfCleaner.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/TranscriptListCleaner.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Progress.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/UnlimitedProgress.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Utils.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/mySql/MySqlTable.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/FileSorter.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCIndex.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCListFilePickle.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/__init__.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Bins.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/SubMapping.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Transcript.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/TranscriptList.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/__init__.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/__init__.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/__init__.pyc |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/Clusterize.xml --- 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 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CollapseReads.xml --- 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 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CompareOverlappingSmallQuery.xml --- 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 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CompareOverlappingSmallRef.xml --- 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 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/ConvertTranscriptFile.xml --- 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 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/removeExonLines.xml --- a/SMART/galaxy/removeExonLines.xml Fri Jan 10 08:59:23 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -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> |
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/removeIntrons.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/removeIntrons.xml Wed Feb 05 11:51:11 2014 -0500 |
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@@ -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> |
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