# HG changeset patch # User m-zytnicki # Date 1391619071 18000 # Node ID 97aa2e42bfdfe3c18a1275c8618d6ffd440db494 # Parent 2ac71607aa60bfdbbf7f6e8999d483140fc42cb1 Uploaded diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/__init__.pyc Binary file SMART/Java/Python/__init__.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/CleanerChooser.pyc Binary file SMART/Java/Python/cleaning/CleanerChooser.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/DefaultCleaner.pyc Binary file SMART/Java/Python/cleaning/DefaultCleaner.pyc has changed 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 @@ -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: diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GffCleaner.pyc Binary file SMART/Java/Python/cleaning/GffCleaner.pyc has changed 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 @@ -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 diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GtfCleaner.pyc Binary file SMART/Java/Python/cleaning/GtfCleaner.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/TranscriptListCleaner.pyc Binary file SMART/Java/Python/cleaning/TranscriptListCleaner.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/__init__.pyc Binary file SMART/Java/Python/cleaning/__init__.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Progress.pyc Binary file SMART/Java/Python/misc/Progress.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/UnlimitedProgress.pyc Binary file SMART/Java/Python/misc/UnlimitedProgress.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Utils.pyc Binary file SMART/Java/Python/misc/Utils.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/__init__.pyc Binary file 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SMART/Java/Python/structure/SubMapping.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Transcript.pyc Binary file SMART/Java/Python/structure/Transcript.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/TranscriptList.pyc Binary file SMART/Java/Python/structure/TranscriptList.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/__init__.pyc Binary file SMART/Java/Python/structure/__init__.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/__init__.pyc Binary file SMART/Java/__init__.pyc has changed diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/__init__.pyc Binary file SMART/__init__.pyc has changed 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 @@ -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 @@ + @@ -49,6 +52,9 @@ + + + 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 @@ -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 @@ + @@ -47,6 +50,9 @@ + + + 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 @@ -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 @@ + @@ -81,6 +86,9 @@ + + + @@ -93,6 +101,7 @@ + @@ -110,6 +119,9 @@ + + + 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 @@ -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 @@ + @@ -81,6 +86,9 @@ + + + @@ -93,6 +101,7 @@ + @@ -110,6 +119,9 @@ + + + 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 @@ -3,33 +3,14 @@ PYTHONPATH - ../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 - - + ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile + - @@ -38,12 +19,12 @@ + + + - - - 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 @@ -1,18 +0,0 @@ - - Removes the lines containing Exon. - - PYTHONPATH - - ../Java/Python/removeExonLines.sh $inputFile > $outputFile - - - - - - - - - - command example: sh removeExonLines.sh input.gff3 - - 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 @@ -0,0 +1,45 @@ + + Removes the introns of the transcript files. + + PYTHONPATH + + ../Java/Python/RemoveExons.py -i $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Simply remove the introns of the input file, thus getting the 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