| Previous changeset 2:8d0de9212f4f (2012-04-20) |
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Commit message:
Uploaded |
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added:
snpEff_2_1a/snpEff_2_1a/._snpEff.config snpEff_2_1a/snpEff_2_1a/._snpEff.jar snpEff_2_1a/snpEff_2_1a/galaxy/._snpEff.xml snpEff_2_1a/snpEff_2_1a/galaxy/._snpEff_download.xml snpEff_2_1a/snpEff_2_1a/galaxy/._snpSift_annotate.xml snpEff_2_1a/snpEff_2_1a/galaxy/._snpSift_caseControl.xml snpEff_2_1a/snpEff_2_1a/galaxy/._snpSift_filter.xml snpEff_2_1a/snpEff_2_1a/galaxy/._snpSift_int.xml snpEff_2_1a/snpEff_2_1a/galaxy/._tool_conf.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpEff_download.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_annotate.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_caseControl.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_int.xml snpEff_2_1a/snpEff_2_1a/galaxy/tool_conf.xml snpEff_2_1a/snpEff_2_1a/scripts/._bam2fastq.pl snpEff_2_1a/snpEff_2_1a/scripts/._buildTestCases.sh snpEff_2_1a/snpEff_2_1a/scripts/._build_regulation.sh snpEff_2_1a/snpEff_2_1a/scripts/._compareToEnsembl.sh snpEff_2_1a/snpEff_2_1a/scripts/._distro.sh snpEff_2_1a/snpEff_2_1a/scripts/._download.sh snpEff_2_1a/snpEff_2_1a/scripts/._fasta2tab.pl snpEff_2_1a/snpEff_2_1a/scripts/._fastaSample.pl snpEff_2_1a/snpEff_2_1a/scripts/._fastaSplit.pl snpEff_2_1a/snpEff_2_1a/scripts/._file2GenomeName.pl snpEff_2_1a/snpEff_2_1a/scripts/._filterOutBoringPredictions.sh snpEff_2_1a/snpEff_2_1a/scripts/._filterOutBoringPredictionsVcf.sh snpEff_2_1a/snpEff_2_1a/scripts/._genesTxtColumnNames.sh snpEff_2_1a/snpEff_2_1a/scripts/._hist.pl snpEff_2_1a/snpEff_2_1a/scripts/._joinSnpEff.pl snpEff_2_1a/snpEff_2_1a/scripts/._nOutOfM.pl snpEff_2_1a/snpEff_2_1a/scripts/._promoterSequences.sh snpEff_2_1a/snpEff_2_1a/scripts/._proteinFasta2NM.pl snpEff_2_1a/snpEff_2_1a/scripts/._qqplot.pl snpEff_2_1a/snpEff_2_1a/scripts/._queue.pl snpEff_2_1a/snpEff_2_1a/scripts/._queue_build.sh snpEff_2_1a/snpEff_2_1a/scripts/._queue_build.txt snpEff_2_1a/snpEff_2_1a/scripts/._queue_build_regulation.txt snpEff_2_1a/snpEff_2_1a/scripts/._queue_dump.txt snpEff_2_1a/snpEff_2_1a/scripts/._queue_test.sh snpEff_2_1a/snpEff_2_1a/scripts/._queue_test.txt snpEff_2_1a/snpEff_2_1a/scripts/._randBedIntervals.pl snpEff_2_1a/snpEff_2_1a/scripts/._sift2vcf.pl snpEff_2_1a/snpEff_2_1a/scripts/._sift2vcf.sh snpEff_2_1a/snpEff_2_1a/scripts/._smoothScatter.pl snpEff_2_1a/snpEff_2_1a/scripts/._snpEff.sh snpEff_2_1a/snpEff_2_1a/scripts/._snpEffM.sh snpEff_2_1a/snpEff_2_1a/scripts/._snpEffXL.sh snpEff_2_1a/snpEff_2_1a/scripts/._snpSift.sh snpEff_2_1a/snpEff_2_1a/scripts/._test.Broad_NS_SYN.sh snpEff_2_1a/snpEff_2_1a/scripts/._uniqCount.pl snpEff_2_1a/snpEff_2_1a/scripts/._vcfEffOnePerLine.pl snpEff_2_1a/snpEff_2_1a/scripts/._vcfSpeedTest.sh snpEff_2_1a/snpEff_2_1a/scripts/bam2fastq.pl snpEff_2_1a/snpEff_2_1a/scripts/buildTestCases.sh snpEff_2_1a/snpEff_2_1a/scripts/build_regulation.sh snpEff_2_1a/snpEff_2_1a/scripts/compareToEnsembl.sh snpEff_2_1a/snpEff_2_1a/scripts/data/GRCh37.64/._countBioTypes.pl snpEff_2_1a/snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/._create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/._fixStartEnd.pl snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/fixStartEnd.pl snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/._convert.pl snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/._convert.sh snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.pl snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.sh snpEff_2_1a/snpEff_2_1a/scripts/data/c_briggsae_WS230/._create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/genomes/._x.sh snpEff_2_1a/snpEff_2_1a/scripts/data/genomes/x.sh snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/._create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/hg19/._create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/hg19/create.sh snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA01/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA01/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA14/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA14/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._mRnaAddParent.pl snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/genes.sh snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl snpEff_2_1a/snpEff_2_1a/scripts/distro.sh snpEff_2_1a/snpEff_2_1a/scripts/download.sh snpEff_2_1a/snpEff_2_1a/scripts/fasta2tab.pl snpEff_2_1a/snpEff_2_1a/scripts/fastaSample.pl snpEff_2_1a/snpEff_2_1a/scripts/fastaSplit.pl snpEff_2_1a/snpEff_2_1a/scripts/file2GenomeName.pl snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictions.sh snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh snpEff_2_1a/snpEff_2_1a/scripts/genesTxtColumnNames.sh snpEff_2_1a/snpEff_2_1a/scripts/hist.pl snpEff_2_1a/snpEff_2_1a/scripts/joinSnpEff.pl snpEff_2_1a/snpEff_2_1a/scripts/nOutOfM.pl snpEff_2_1a/snpEff_2_1a/scripts/promoterSequences.sh snpEff_2_1a/snpEff_2_1a/scripts/proteinFasta2NM.pl snpEff_2_1a/snpEff_2_1a/scripts/qqplot.pl snpEff_2_1a/snpEff_2_1a/scripts/queue.pl snpEff_2_1a/snpEff_2_1a/scripts/queue_build.sh snpEff_2_1a/snpEff_2_1a/scripts/queue_build.txt snpEff_2_1a/snpEff_2_1a/scripts/queue_build_regulation.txt snpEff_2_1a/snpEff_2_1a/scripts/queue_dump.txt snpEff_2_1a/snpEff_2_1a/scripts/queue_test.sh snpEff_2_1a/snpEff_2_1a/scripts/queue_test.txt snpEff_2_1a/snpEff_2_1a/scripts/randBedIntervals.pl snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.pl snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.sh snpEff_2_1a/snpEff_2_1a/scripts/smoothScatter.pl snpEff_2_1a/snpEff_2_1a/scripts/snpEff.sh snpEff_2_1a/snpEff_2_1a/scripts/snpEffM.sh snpEff_2_1a/snpEff_2_1a/scripts/snpEffXL.sh snpEff_2_1a/snpEff_2_1a/scripts/snpSift.sh snpEff_2_1a/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh snpEff_2_1a/snpEff_2_1a/scripts/uniqCount.pl snpEff_2_1a/snpEff_2_1a/scripts/vcfEffOnePerLine.pl snpEff_2_1a/snpEff_2_1a/scripts/vcfSpeedTest.sh snpEff_2_1a/snpEff_2_1a/snpEff.config snpEff_2_1a/snpEff_2_1a/snpEff.jar |
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removed:
snpEff_2_1a/._snpEff.config snpEff_2_1a/._snpEff.jar snpEff_2_1a/galaxy/._snpEff.xml snpEff_2_1a/galaxy/._snpEff_download.xml snpEff_2_1a/galaxy/._snpSift_annotate.xml snpEff_2_1a/galaxy/._snpSift_caseControl.xml snpEff_2_1a/galaxy/._snpSift_filter.xml snpEff_2_1a/galaxy/._snpSift_int.xml snpEff_2_1a/galaxy/._tool_conf.xml snpEff_2_1a/galaxy/snpEff.xml snpEff_2_1a/galaxy/snpEff_download.xml snpEff_2_1a/galaxy/snpSift_annotate.xml snpEff_2_1a/galaxy/snpSift_caseControl.xml snpEff_2_1a/galaxy/snpSift_filter.xml snpEff_2_1a/galaxy/snpSift_int.xml snpEff_2_1a/galaxy/tool_conf.xml snpEff_2_1a/scripts/._bam2fastq.pl snpEff_2_1a/scripts/._buildTestCases.sh snpEff_2_1a/scripts/._build_regulation.sh snpEff_2_1a/scripts/._compareToEnsembl.sh snpEff_2_1a/scripts/._distro.sh snpEff_2_1a/scripts/._download.sh snpEff_2_1a/scripts/._fasta2tab.pl snpEff_2_1a/scripts/._fastaSample.pl snpEff_2_1a/scripts/._fastaSplit.pl snpEff_2_1a/scripts/._file2GenomeName.pl snpEff_2_1a/scripts/._filterOutBoringPredictions.sh snpEff_2_1a/scripts/._filterOutBoringPredictionsVcf.sh snpEff_2_1a/scripts/._genesTxtColumnNames.sh snpEff_2_1a/scripts/._hist.pl snpEff_2_1a/scripts/._joinSnpEff.pl snpEff_2_1a/scripts/._nOutOfM.pl snpEff_2_1a/scripts/._promoterSequences.sh snpEff_2_1a/scripts/._proteinFasta2NM.pl snpEff_2_1a/scripts/._qqplot.pl snpEff_2_1a/scripts/._queue.pl snpEff_2_1a/scripts/._queue_build.sh snpEff_2_1a/scripts/._queue_build.txt snpEff_2_1a/scripts/._queue_build_regulation.txt snpEff_2_1a/scripts/._queue_dump.txt snpEff_2_1a/scripts/._queue_test.sh snpEff_2_1a/scripts/._queue_test.txt snpEff_2_1a/scripts/._randBedIntervals.pl snpEff_2_1a/scripts/._sift2vcf.pl snpEff_2_1a/scripts/._sift2vcf.sh snpEff_2_1a/scripts/._smoothScatter.pl snpEff_2_1a/scripts/._snpEff.sh snpEff_2_1a/scripts/._snpEffM.sh snpEff_2_1a/scripts/._snpEffXL.sh snpEff_2_1a/scripts/._snpSift.sh snpEff_2_1a/scripts/._test.Broad_NS_SYN.sh snpEff_2_1a/scripts/._uniqCount.pl snpEff_2_1a/scripts/._vcfEffOnePerLine.pl snpEff_2_1a/scripts/._vcfSpeedTest.sh snpEff_2_1a/scripts/bam2fastq.pl snpEff_2_1a/scripts/buildTestCases.sh snpEff_2_1a/scripts/build_regulation.sh snpEff_2_1a/scripts/compareToEnsembl.sh snpEff_2_1a/scripts/data/GRCh37.64/._countBioTypes.pl snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl snpEff_2_1a/scripts/data/SL2.40/._create.sh snpEff_2_1a/scripts/data/SL2.40/._fixStartEnd.pl snpEff_2_1a/scripts/data/SL2.40/create.sh snpEff_2_1a/scripts/data/SL2.40/fixStartEnd.pl snpEff_2_1a/scripts/data/alyrata1/._convert.pl snpEff_2_1a/scripts/data/alyrata1/._convert.sh snpEff_2_1a/scripts/data/alyrata1/convert.pl snpEff_2_1a/scripts/data/alyrata1/convert.sh snpEff_2_1a/scripts/data/c_briggsae_WS230/._create.sh snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh snpEff_2_1a/scripts/data/genomes/._x.sh snpEff_2_1a/scripts/data/genomes/x.sh snpEff_2_1a/scripts/data/gmax1.09v8/._create.sh snpEff_2_1a/scripts/data/gmax1.09v8/create.sh snpEff_2_1a/scripts/data/hg19/._create.sh snpEff_2_1a/scripts/data/hg19/create.sh snpEff_2_1a/scripts/data/paeru.PA01/._genes.sh snpEff_2_1a/scripts/data/paeru.PA01/genes.sh snpEff_2_1a/scripts/data/paeru.PA14/._genes.sh snpEff_2_1a/scripts/data/paeru.PA14/genes.sh snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/._genes.sh snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/._genes.sh snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh snpEff_2_1a/scripts/data/ppersica139/._genes.sh snpEff_2_1a/scripts/data/ppersica139/genes.sh snpEff_2_1a/scripts/data/rice5/._genes.sh snpEff_2_1a/scripts/data/rice5/._mRnaAddParent.pl snpEff_2_1a/scripts/data/rice5/genes.sh snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl snpEff_2_1a/scripts/distro.sh snpEff_2_1a/scripts/download.sh snpEff_2_1a/scripts/fasta2tab.pl snpEff_2_1a/scripts/fastaSample.pl snpEff_2_1a/scripts/fastaSplit.pl snpEff_2_1a/scripts/file2GenomeName.pl snpEff_2_1a/scripts/filterOutBoringPredictions.sh snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh snpEff_2_1a/scripts/genesTxtColumnNames.sh snpEff_2_1a/scripts/hist.pl snpEff_2_1a/scripts/joinSnpEff.pl snpEff_2_1a/scripts/nOutOfM.pl snpEff_2_1a/scripts/promoterSequences.sh snpEff_2_1a/scripts/proteinFasta2NM.pl snpEff_2_1a/scripts/qqplot.pl snpEff_2_1a/scripts/queue.pl snpEff_2_1a/scripts/queue_build.sh snpEff_2_1a/scripts/queue_build.txt snpEff_2_1a/scripts/queue_build_regulation.txt snpEff_2_1a/scripts/queue_dump.txt snpEff_2_1a/scripts/queue_test.sh snpEff_2_1a/scripts/queue_test.txt snpEff_2_1a/scripts/randBedIntervals.pl snpEff_2_1a/scripts/sift2vcf.pl snpEff_2_1a/scripts/sift2vcf.sh snpEff_2_1a/scripts/smoothScatter.pl snpEff_2_1a/scripts/snpEff.sh snpEff_2_1a/scripts/snpEffM.sh snpEff_2_1a/scripts/snpEffXL.sh snpEff_2_1a/scripts/snpSift.sh snpEff_2_1a/scripts/test.Broad_NS_SYN.sh snpEff_2_1a/scripts/uniqCount.pl snpEff_2_1a/scripts/vcfEffOnePerLine.pl snpEff_2_1a/scripts/vcfSpeedTest.sh snpEff_2_1a/snpEff.config snpEff_2_1a/snpEff.jar |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpEff.xml --- a/snpEff_2_1a/galaxy/snpEff.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,482 +0,0 @@\n-<tool id="snpEff" name="SnpEff" version="1.0">\n-\t<description>Variant efefct and annotation</description>\n-\t<!-- \n-\t You will need to change the path to wherever your installation is.\n-\t\tYou can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)\n-\t<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>\n-\t-->\n-\t<command>java -Xmx6G -jar /Users/pablocingolani/snpEff/snpEff.jar eff -c /Users/pablocingolani/snpEff/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>\n-\t<inputs>\n-\t\t<param format="Tabular" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>\n-\n-\t\t<param name="inputFormat" type="select" label="Input format">\n-\t\t\t<option value="vcf">VCF</option>\n-\t\t\t<option value="txt">Tabular</option>\n-\t\t\t<option value="pileup">Pileup</option>\n-\t\t\t<option value="bed">BED</option>\n-\t\t</param>\n-\n-\t\t<param name="outputFormat" type="select" label="Output format">\n-\t\t\t<option value="txt">Tabular</option>\n-\t\t\t<option value="vcf">VCF (only if input is VCF)</option>\n-\t\t\t<option value="bed">BED</option>\n-\t\t\t<option value="bedAnn">BED Annotations</option>\n-\t\t</param>\n-\n-\t\t<param name="genomeVersion" type="select" label="Genome">\n-\t\t\t\t<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>\n-\t\t\t\t<option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option>\n-\t\t\t\t<option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option>\n-\t\t\t\t<option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option>\n-\t\t\t\t<option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option>\n-\t\t\t\t<option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option>\n-\t\t\t\t<option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option>\n-\t\t\t\t<option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option>\n-\t\t\t\t<option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option>\n-\t\t\t\t<option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option>\n-\t\t\t\t<option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option>\n-\t\t\t\t<option value="agam2.6">Anopheles gambiae : agam2.6</option>\n-\t\t\t\t<option value="agam">Anopheles gambiae : agam</option>\n-\t\t\t\t<option value="aquiCoer">Aquilegia coerulea : aquiCoer</option>\n-\t\t\t\t<option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option>\n-\t\t\t\t<option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option>\n-\t\t\t\t<option value="athaliana130">Arabidopsis Thaliana : athaliana130</option>\n-\t\t\t\t<option value="alyrata107">Arabidopsis lyrata : alyrata107</option>\n-\t\t\t\t<option value="alyrata1">Arabidopsis lyrata : alyrata1</option>\n-\t\t\t\t<option value="amel2">Bee : amel2</option>\n-\t\t\t\t<option value="btau4.0.61">Bos taurus : btau4.0.61</option>\n-\t\t\t\t<option value="btau4.0.60">Bos taurus : btau4.0.60</option>\n-\t\t\t\t<option value="btau4.0.59">Bos taurus : btau4.0.59</option>\n-\t\t\t\t<option value="UMD3_1">Bos taurus : UMD3_1</option>\n-\t\t\t\t<option value="UMD3.1.66">Bos taurus : UMD3.1.66</option>\n-\t\t\t\t<option value="UMD3.1.65">Bos taurus : UMD3.1.65</option>\n-\t\t\t\t<option value="UMD3.1.64">Bos taurus : UMD3.1.64</option>\n-\t\t\t\t<option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option>\n-\t\t\t\t<option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option>\n-\t\t\t\t<option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option>\n-\t\t\t\t<option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option>\n-\t\t\t\t<option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option>\n-\t\t\t\t<option value="WS220.66">Caenorhabditis elegans : WS220.66</option>\n-\t\t\t\t<option value="WS220.65">Caenorhabditis elegans : WS220.'..b' belangeri : TREESHREW.63</option>\n-\t\t\t\t<option value="turTru1.66">Tursiops truncatus : turTru1.66</option>\n-\t\t\t\t<option value="turTru1.65">Tursiops truncatus : turTru1.65</option>\n-\t\t\t\t<option value="turTru1.64">Tursiops truncatus : turTru1.64</option>\n-\t\t\t\t<option value="turTru1.63">Tursiops truncatus : turTru1.63</option>\n-\t\t\t\t<option value="turTru1.61">Tursiops truncatus : turTru1.61</option>\n-\t\t\t\t<option value="turTru1.60">Tursiops truncatus : turTru1.60</option>\n-\t\t\t\t<option value="vacwr">Vaccinia Western Reserve : vacwr</option>\n-\t\t\t\t<option value="vibrio">Vibrio Cholerae : vibrio</option>\n-\t\t\t\t<option value="vicPac1.66">Vicugna pacos : vicPac1.66</option>\n-\t\t\t\t<option value="vicPac1.65">Vicugna pacos : vicPac1.65</option>\n-\t\t\t\t<option value="vicPac1.64">Vicugna pacos : vicPac1.64</option>\n-\t\t\t\t<option value="vicPac1.63">Vicugna pacos : vicPac1.63</option>\n-\t\t\t\t<option value="vicPac1.61">Vicugna pacos : vicPac1.61</option>\n-\t\t\t\t<option value="vicPac1.60">Vicugna pacos : vicPac1.60</option>\n-\t\t\t\t<option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option>\n-\t\t\t\t<option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option>\n-\t\t\t\t<option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option>\n-\t\t\t\t<option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option>\n-\t\t\t\t<option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option>\n-\t\t\t\t<option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option>\n-\t\t</param>\n-\n-\t\t<param name="udLength" type="select" label="Upstream / Downstream length">\n-\t\t\t<option value="0">No upstream / downstream intervals (0 bases)</option>\n-\t\t\t<option value="200">200 bases</option>\n-\t\t\t<option value="500">500 bases</option>\n-\t\t\t<option value="1000">1000 bases</option>\n-\t\t\t<option value="2000">2000 bases</option>\n-\t\t\t<option value="5000" selected="true">5000 bases</option>\n-\t\t\t<option value="10000">10000 bases</option>\n-\t\t\t<option value="20000">20000 bases</option>\n-\t\t</param>\n-\n- <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">\n-\t\t\t<option value="">No filter (analyze everything)</option>\n-\t\t\t<option value="-hom">Analyze homozygous sequence changes only </option>\n-\t\t\t<option value="-het">Analyze heterozygous sequence changes only </option>\n- </param>\n-\n- <param name="filterIn" type="select" display="radio" label="Filter sequence changes">\n-\t\t\t<option value="">No filter (analyze everything)</option>\n-\t\t\t<option value="-del">Analyze deletions only </option>\n-\t\t\t<option value="-ins">Analyze insertions only </option>\n-\t\t\t<option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>\n-\t\t\t<option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>\n- </param>\n-\n- <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">\n-\t\t\t<option value="None" selected="true">None</option>\n-\t\t\t<option value="downstream">Do not show DOWNSTREAM changes </option>\n-\t\t\t<option value="intergenic">Do not show INTERGENIC changes </option>\n-\t\t\t<option value="intron">Do not show INTRON changes </option>\n-\t\t\t<option value="upstream">Do not show UPSTREAM changes </option>\n-\t\t\t<option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>\n- </param>\n-\n- <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">\n-\t\t\t<option value="">Use default (based on input type)</option>\n-\t\t\t<option value="-0">Force zero-based positions (both input and output)</option>\n-\t\t\t<option value="-1">Force one-based positions (both input and output)</option>\n-\t\t</param>\n-\t</inputs>\n-\t<outputs>\n-\t\t<data format="tabular" name="output" />\n-\t\t<data format="html" name="statsFile" />\n-\t</outputs>\n-\n-\t<help>\n-\n-This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.\n-\n-For details about this tool, please go to http://snpEff.sourceforge.net\n-\n-\t</help>\n-</tool>\n-\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpEff_download.xml --- a/snpEff_2_1a/galaxy/snpEff_download.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,421 +0,0 @@\n-<tool id="snpEff_download" name="SnpEff Download" version="1.0">\n-\t<description>Download a new database</description>\n-\t<command>java -jar /Users/pablocingolani/snpEff/snpEff.jar download -c /Users/pablocingolani/snpEff/snpEff.config $genomeVersion > $logfile </command>\n-\t<inputs>\n-\t\t<param name="genomeVersion" type="select" label="Genome">\n-\t\t\t\t<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>\n-\t\t\t\t<option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option>\n-\t\t\t\t<option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option>\n-\t\t\t\t<option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option>\n-\t\t\t\t<option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option>\n-\t\t\t\t<option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option>\n-\t\t\t\t<option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option>\n-\t\t\t\t<option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option>\n-\t\t\t\t<option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option>\n-\t\t\t\t<option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option>\n-\t\t\t\t<option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option>\n-\t\t\t\t<option value="agam2.6">Anopheles gambiae : agam2.6</option>\n-\t\t\t\t<option value="agam">Anopheles gambiae : agam</option>\n-\t\t\t\t<option value="aquiCoer">Aquilegia coerulea : aquiCoer</option>\n-\t\t\t\t<option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option>\n-\t\t\t\t<option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option>\n-\t\t\t\t<option value="athaliana130">Arabidopsis Thaliana : athaliana130</option>\n-\t\t\t\t<option value="alyrata107">Arabidopsis lyrata : alyrata107</option>\n-\t\t\t\t<option value="alyrata1">Arabidopsis lyrata : alyrata1</option>\n-\t\t\t\t<option value="amel2">Bee : amel2</option>\n-\t\t\t\t<option value="btau4.0.61">Bos taurus : btau4.0.61</option>\n-\t\t\t\t<option value="btau4.0.60">Bos taurus : btau4.0.60</option>\n-\t\t\t\t<option value="btau4.0.59">Bos taurus : btau4.0.59</option>\n-\t\t\t\t<option value="UMD3_1">Bos taurus : UMD3_1</option>\n-\t\t\t\t<option value="UMD3.1.66">Bos taurus : UMD3.1.66</option>\n-\t\t\t\t<option value="UMD3.1.65">Bos taurus : UMD3.1.65</option>\n-\t\t\t\t<option value="UMD3.1.64">Bos taurus : UMD3.1.64</option>\n-\t\t\t\t<option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option>\n-\t\t\t\t<option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option>\n-\t\t\t\t<option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option>\n-\t\t\t\t<option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option>\n-\t\t\t\t<option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option>\n-\t\t\t\t<option value="WS220.66">Caenorhabditis elegans : WS220.66</option>\n-\t\t\t\t<option value="WS220.65">Caenorhabditis elegans : WS220.65</option>\n-\t\t\t\t<option value="WS220.64">Caenorhabditis elegans : WS220.64</option>\n-\t\t\t\t<option value="WS220.63">Caenorhabditis elegans : WS220.63</option>\n-\t\t\t\t<option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option>\n-\t\t\t\t<option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option>\n-\t\t\t\t<option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option>\n-\t\t\t\t<option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option>\n-\t\t\t\t<option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option>\n-\t\t\t\t<option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option>\n-\t\t\t\t<option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option>\n-\t\t\t\t<option value="canFam2.61">Canis familiaris : canFam2.61</option>\n-\t\t\t\t<option value="canFam2.60">Canis familiaris : canFam2.60</option>\n-\t\t\t\t<option value="canFam2.59">Canis familiaris : canFam2.59</option>\n-\t\t\t\t<option value="BROADD2.66">Canis familiaris : BROADD2.66</option>\n-\t\t\t\t<option value="BROADD2.65">Canis familiaris : BROADD2.65</option>\n-\t\t\t\t<option value="BROADD2.64">Canis familiaris : BROADD2.64</option>\n-\t\t\t\t<option '..b'pes : fugu4.60</option>\n-\t\t\t\t<option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option>\n-\t\t\t\t<option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option>\n-\t\t\t\t<option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option>\n-\t\t\t\t<option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option>\n-\t\t\t\t<option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option>\n-\t\t\t\t<option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option>\n-\t\t\t\t<option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option>\n-\t\t\t\t<option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option>\n-\t\t\t\t<option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option>\n-\t\t\t\t<option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option>\n-\t\t\t\t<option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option>\n-\t\t\t\t<option value="testHg3765Chr22">TestCase : testHg3765Chr22</option>\n-\t\t\t\t<option value="testHg3763ChrY">TestCase : testHg3763ChrY</option>\n-\t\t\t\t<option value="testHg3763Chr20">TestCase : testHg3763Chr20</option>\n-\t\t\t\t<option value="testHg3763Chr1">TestCase : testHg3763Chr1</option>\n-\t\t\t\t<option value="testHg3761Chr16">TestCase : testHg3761Chr16</option>\n-\t\t\t\t<option value="testHg3761Chr15">TestCase : testHg3761Chr15</option>\n-\t\t\t\t<option value="testCase">TestCase : testCase</option>\n-\t\t\t\t<option value="test">TestCase : test</option>\n-\t\t\t\t<option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option>\n-\t\t\t\t<option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option>\n-\t\t\t\t<option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option>\n-\t\t\t\t<option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option>\n-\t\t\t\t<option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option>\n-\t\t\t\t<option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option>\n-\t\t\t\t<option value="SL2.40">Tomato : SL2.40</option>\n-\t\t\t\t<option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option>\n-\t\t\t\t<option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option>\n-\t\t\t\t<option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option>\n-\t\t\t\t<option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option>\n-\t\t\t\t<option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option>\n-\t\t\t\t<option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option>\n-\t\t\t\t<option value="turTru1.66">Tursiops truncatus : turTru1.66</option>\n-\t\t\t\t<option value="turTru1.65">Tursiops truncatus : turTru1.65</option>\n-\t\t\t\t<option value="turTru1.64">Tursiops truncatus : turTru1.64</option>\n-\t\t\t\t<option value="turTru1.63">Tursiops truncatus : turTru1.63</option>\n-\t\t\t\t<option value="turTru1.61">Tursiops truncatus : turTru1.61</option>\n-\t\t\t\t<option value="turTru1.60">Tursiops truncatus : turTru1.60</option>\n-\t\t\t\t<option value="vacwr">Vaccinia Western Reserve : vacwr</option>\n-\t\t\t\t<option value="vibrio">Vibrio Cholerae : vibrio</option>\n-\t\t\t\t<option value="vicPac1.66">Vicugna pacos : vicPac1.66</option>\n-\t\t\t\t<option value="vicPac1.65">Vicugna pacos : vicPac1.65</option>\n-\t\t\t\t<option value="vicPac1.64">Vicugna pacos : vicPac1.64</option>\n-\t\t\t\t<option value="vicPac1.63">Vicugna pacos : vicPac1.63</option>\n-\t\t\t\t<option value="vicPac1.61">Vicugna pacos : vicPac1.61</option>\n-\t\t\t\t<option value="vicPac1.60">Vicugna pacos : vicPac1.60</option>\n-\t\t\t\t<option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option>\n-\t\t\t\t<option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option>\n-\t\t\t\t<option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option>\n-\t\t\t\t<option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option>\n-\t\t\t\t<option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option>\n-\t\t\t\t<option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option>\n-\t\t</param>\n-\t</inputs>\n-\n-\t<outputs>\n-\t\t<data format="txt" name="logfile" />\n-\t</outputs>\n-\n-\t<help>\n-\n-This tool downloads a SnpEff database.\n-\n-For details about this tool, please go to http://snpEff.sourceforge.net\n-\n-\t</help>\n-</tool>\n-\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpSift_annotate.xml --- a/snpEff_2_1a/galaxy/snpSift_annotate.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0"> - <description>Annotate SNPs from dbSnp</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <command>java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar annotate -q $dbSnp $input > $output </command> - <inputs> - <param format="Tabular" name="input" type="data" label="VCF input"/> - <param format="Tabular" name="dbSnp" type="data" label="dbSnp in VCF format"/> - </inputs> - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <help> - -This is typically used to annotate IDs from dbSnp. - -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate - - </help> -</tool> - |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpSift_caseControl.xml --- a/snpEff_2_1a/galaxy/snpSift_caseControl.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,35 +0,0 @@ -<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0"> - <description>Count samples are in 'case' and 'control' groups.</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <command> - java -Xmx1G -jar /home/pcingola/tools/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output - </command> - <inputs> - <param format="Tabular" name="input" type="data" label="VCF input"/> - <param name="hhCase" type="select" label="Hom/Het case"> - <option value="any">Any</option> - <option value="hom">Homozygous</option> - <option value="het">Heterozygous</option> - </param> - <param name="hhControl" type="select" label="Hom/Het control"> - <option value="any">Any</option> - <option value="hom">Homozygous</option> - <option value="het">Heterozygous</option> - </param> - <param name="caseControStr" type="text" label="Case / Control" size="50"/> - </inputs> - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <help> - -Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file. - -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol - - </help> -</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpSift_filter.xml --- a/snpEff_2_1a/galaxy/snpSift_filter.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,33 +0,0 @@ -<tool id="snpSift_filter" name="SnpSift Filter" version="1.0"> - <options sanitize="False" /> - <description>Filter variants using arbitrary expressions</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output - --> - <command> - java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output - </command> - <inputs> - <param format="Tabular" name="input" type="data" label="VCF input"/> - <param name="expr" type="text" label="Expression" size="50"/> - </inputs> - <configfiles> - <configfile name="exprFile"> - $expr - </configfile> - </configfiles> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <help> - -You can filter using arbitrary expressions. - -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter - - </help> -</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/snpSift_int.xml --- a/snpEff_2_1a/galaxy/snpSift_int.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="1.0"> - <description>Filter variants using intervals </description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <command> - cat $input | java -Xmx2G -jar /home/pcingola/tools/SnpSift.jar int $bedFile > $output - </command> - <inputs> - <param format="Tabular" name="input" type="data" label="VCF input"/> - <param format="Tabular" name="bedFile" type="data" label="Intervals (BED file)"/> - </inputs> - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <help> - -You can filter using intervals (BED file) - -For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals - - </help> -</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/galaxy/tool_conf.xml --- a/snpEff_2_1a/galaxy/tool_conf.xml Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ - - <!-- - Add this section to tool_conf.xml file in your Galaxy distribution - --> - <section name="SnpEff tools" id="snpEff_tools"> - <tool file="snpEff/snpEff.xml" /> - <tool file="snpEff/snpEff_download.xml" /> - <tool file="snpEff/snpSift_annotate.xml" /> - <tool file="snpEff/snpSift_caseControl.xml" /> - <tool file="snpEff/snpSift_filter.xml" /> - <tool file="snpEff/snpSift_int.xml" /> - </section> - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/bam2fastq.pl --- a/snpEff_2_1a/scripts/bam2fastq.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/usr/bin/perl - -while( $l = <STDIN> ) { - chomp $l; - @t = split /\t/, $l; - print "\@$t[0]\n$t[9]\n+\n$t[10]\n"; -} - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/buildTestCases.sh --- a/snpEff_2_1a/scripts/buildTestCases.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -#!/bin/sh - -# Test cases hg37 -./scripts/snpEffM.sh build -v -txt testCase - -# Test cases hg37.61 -./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr15 -./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr16 - -# Test cases hg37.63 -./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr1 -./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr20 -./scripts/snpEffM.sh build -v -gtf22 testHg3763ChrY - -# Test cases hg37.65 -./scripts/snpEffM.sh build -v -gtf22 testHg3765Chr22 |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/build_regulation.sh --- a/snpEff_2_1a/scripts/build_regulation.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -#!/bin/sh - -./scripts/queue.pl 10 24 15 queue_build_regulation.txt - - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/compareToEnsembl.sh --- a/snpEff_2_1a/scripts/compareToEnsembl.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff/ - -java -Xmx3G \ - -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ - ca.mcgill.mcb.pcingola.testCases.CompareToEnsembl \ - $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl --- a/snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,71 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# -# Count unmber of bioType for transcript (second column in GTF file) and -# for gene ('/gene_biotype' info field) -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -use strict; - -my($count, %count, $countMatch) = (0, 0); - -#--- -# Process input (GTF file) -#--- -my($l, $key, $field, @t, %bioType); -while( $l = <STDIN> ) { - chomp $l; - @t = split /\t/, $l; - - # Get transcript biotype - my($bioTypeTr) = $t[1]; - die "Cannot find biotype" if( $bioTypeTr eq '' ); - - # Get gene biotype - @t = split /;/, $t[8]; - my($bioTypeGene) = ''; - foreach $field ( @t ) { - # Parse 'name value' fields - if( $field =~/\s*(.*)\s\"(.*)\"/ ) { - my($name, $value) = ($1, $2); - if( $name eq 'gene_biotype' ) { $bioTypeGene = $value; } - } - } - die "Cannot find biotype" if($bioTypeGene eq ''); - - $bioType{$bioTypeTr} = 1; - $bioType{$bioTypeGene} = 1; - - $key = "$bioTypeTr\t$bioTypeGene"; - $count{$key}++; - - # Count - if( $bioTypeTr eq $bioTypeGene ) { $countMatch++; } - $count++; -} - -#--- -# Show results -#--- -foreach $key ( sort keys %count ) { print "$count{$key}\t$key\n"; } -print "Count\t$count\n"; -print "Count match\t$countMatch\n"; - -#--- -# Show as table -#--- -my($bt, $bg); -print "\t"; -foreach $bg ( sort keys %bioType ) { print "$bg\t"; } -print "\n"; -foreach $bt ( sort keys %bioType ) { - print "$bt\t"; - foreach $bg ( sort keys %bioType ) { - $key = "$bt\t$bg"; - print "$count{$key}\t"; - } - print "\n"; -} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/SL2.40/create.sh --- a/snpEff_2_1a/scripts/data/SL2.40/create.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,26 +0,0 @@ -#!/bin/sh - -# wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz - -# GFF has to be downloaded manually from -# -# http://solgenomics.net/itag/release/2.3/list_files# -# File ITAG2.3_gene_models.gff3 -# -# - -# Create genes.gff -echo Decompressing the file -cp ITAG2.3_gene_models.gff3.gz genes.gff.gz -rm -f genes.gff -gunzip genes.gff.gz - -echo Fixing start-end problem -cat genes.gff | ./fixStartEnd.pl > g -mv g genes.gff - -# Append FASTA Sequences -echo "###" >> genes.gff -echo "##FASTA" >> genes.gff -zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff - |
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| @@ -1,19 +0,0 @@ -#!/usr/bin/perl - -# -# If start > end swap values -# -while( $l = <STDIN> ) { - chomp $l; - @t = (); - @t = split /\t/, $l; - - ($start, $end) = ($t[3], $t[4]); - if( $start > $end ) { - #print STDERR "ERROR:\t$l\n"; - ($t[3], $t[4]) = ($t[4], $t[3]); - $l = join "\t", @t; - } - - print "$l\n"; -} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/alyrata1/convert.pl --- a/snpEff_2_1a/scripts/data/alyrata1/convert.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,56 +0,0 @@ -#!/usr/bin/perl - - -# Parse command line argument -$gtfFile = $ARGV[0]; - -#--- -# Pass one: Get geneID -> transcriptID -# Note: It is assumed (and it is true for this particular file) that each genes has only one transcript -# This assumption os obviously not true for other files & other organisms -#---- -print STDERR "Pass 1: Read IDs\n"; -open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; - -while( $l = <GTF> ) { - chomp $l; - ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; - - $gid = $tid = ""; - if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } - if( $attr =~ /transcript_id "(.*?)";/ ) { $tid = $1; } - - if(( $gid ne '' ) && ( $tid ne '' )) { - # print "\tgid = $gid\n\ttid = $tid\n"; - - # Store transcriptId - if( $tbyg{$gid} eq '' ) { $tbyg{$gid} = $tid; } - - # Is there more than one transcript per gene? => Error - if( $tbyg{$gid} ne $tid ) { die "Error: More than one transcript per gene. We cannot map transcripts!\n\t$tid ne $tbyg{$gid}\n"; } - } -} - -close GTF; - -#--- -# Pass two: Fill in the missing transcript IDs -#--- -print STDERR "Pass 2: Add ID data\n"; -open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; - -while( $l = <GTF> ) { - chomp $l; - ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; - - $gid = ""; - if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } - elsif( $attr =~ /gene_id "(.*)"/ ) { $gid = $1; } - else { print STDERR "Cannot match '$attr'\n"; } - $tid = $tbyg{$gid}; - - if(( $gid ne '' ) && ( $tid ne '' )) { print "$seqname\t$source\t$feature\t$start\t$end\t$score\t$strand\t$frame\tgene_id \"$gid\"; transcript_id \"$tid\";\n"; } - else { print STDERR "Skipping line: $l\n\tgid = '$gid'\n\ttid = '$tid'\n"; } -} - -close GTF; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/alyrata1/convert.sh --- a/snpEff_2_1a/scripts/data/alyrata1/convert.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ -#!/bin/sh - -zcat Araly1_GeneModels_FilteredModels6.gff.gz \ - | sed "s/name/gene_id/" \ - | sed "s/transcriptId \(.*\)/transcript_id \"\1\";/" \ - | sed "s/exonNumber \(.*\)/exon_number \"\1\";/" \ - > g1 - -./convert.pl g1 > genes.gtf -rm -vf g1 - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/c_briggsae_WS230/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh --- a/snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -#!/bin/sh -e - -zcat c_briggsae.WS230.annotations.gff3.gz \ - | grep -v SNP \ - | grep -v translated_nucleotide_match \ - | grep -v repeat_region \ - | grep -v inverted_repeat \ - | grep -v tandem_repeat \ - | grep -v nucleotide_match \ - > genes.gff - -# Add fasta sequence -echo "###" >> genes.gff -echo "##FASTA" >> genes.gff -zcat c_briggsae.WS230.genomic.fa.gz >> genes.gff |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/genomes/._x.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/genomes/x.sh --- a/snpEff_2_1a/scripts/data/genomes/x.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/bin/sh - -for chr in chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr1.fa chr20.fa chr21.fa chr22.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chrMT.fa chrX.fa chrY.fa -do - MDGR=`cat GRCh37.65/$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` - MDHG=`cat hg19/chr$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` - echo -e "$chr\n\t$MDGR\n\t$MDHG" -done |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/gmax1.09v8/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/gmax1.09v8/create.sh --- a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,35 +0,0 @@ -#!/bin/sh -e - -echo "Processing GFF file" -gunzip -c Gmax_109_gene.gff3.gz > genes.gff -# | sed "s/.five_prime_UTR.1//" \ -# | sed "s/.three_prime_UTR.1//" \ -# > genes.gff - -echo "Adding FASTA sequence" -( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff - -ehco "Create CDS file" -gunzip -c Gmax_109_cds.fa.gz \ - | sed "s/|PACid:/|PAC:/" \ - | sed "s/Glyma.*|//" \ - > cds.fa - -echo "Create protein file" -gunzip -c Gmax_109_peptide.fa.gz \ - | sed "s/|PACid:/|PAC:/" \ - | sed "s/Glyma.*|//" \ - > protein.fa - -# Build databse -cd $HOME/snpEff - -./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build - -# CDS test -./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds - -cd - - -echo Done! - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/hg19/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/hg19/create.sh --- a/snpEff_2_1a/scripts/data/hg19/create.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,52 +0,0 @@ -#!/bin/sh - -REF=hg19 - -#--- -# Download latest datasets -#--- - -# # Genome sequence -# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/bigZips/chromFa.tar.gz -# -# # Protein sequences -# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz -# -# # CDS sequences -# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz -# -# # RefLink -# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/database/refLink.txt.gz -# -# #--- -# # Create files -# #--- -# gunzip refLink.txt.gz -# -# # Protein fasta -# zcat human.protein.faa.gz | ../../scripts/proteinFasta2NM.pl refLink.txt > protein.fa -# gzip protein.fa -# -# # CDS fasta -# zcat human.rna.fna.gz | sed "s/^>gi|[0-9]*|ref|\(.*\)\..*|.*/>\1/" > cds.fa -# gzip cds.fa - -# Chromosome fasta -#rm -rvf chr -#mkdir chr -cd chr -#tar -xvzf ../chromFa.tar.gz - -FASTA=../$REF.fa -echo Creating FASTA file -rm -vf $FASTA -cat chr[1-9].fa >> $FASTA -cat chr??.fa >> $FASTA -cat chr[A-Z].fa >> $FASTA -cat chr???*.fa >> $FASTA - -cd - - -# # Compress genome file -# $HOME/tools/pigz/pigz hg19.fa -# cp hg19.fa.gz $HOME/snpEff/data/genomes/ |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/paeru.PA01/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/paeru.PA01/genes.sh --- a/snpEff_2_1a/scripts/data/paeru.PA01/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#!/bin/sh - -cat NC_002516.2.gff | sed "s/CDS/exon/" > genes.gff -echo "##FASTA" >> genes.gff -cat NC_002516.2.fna >> genes.gff - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/paeru.PA14/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/paeru.PA14/genes.sh --- a/snpEff_2_1a/scripts/data/paeru.PA14/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#!/bin/sh - -cat NC_008463.1.gff | sed "s/CDS/exon/" > genes.gff -echo "##FASTA" >> genes.gff -cat NC_008463.1.fna >> genes.gff - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh --- a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#!/bin/sh - -cat NC_009444.1.gff | sed "s/CDS/exon/" > genes.gff -echo "##FASTA" >> genes.gff -cat NC_009444.1.fna >> genes.gff - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh --- a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#!/bin/sh - -cat NC_012660.1.gff | sed "s/CDS/exon/" > genes.gff -echo "##FASTA" >> genes.gff -cat NC_012660.1.fna >> genes.gff - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/ppersica139/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/ppersica139/genes.sh --- a/snpEff_2_1a/scripts/data/ppersica139/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/bin/sh - -# Download files -#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139.fa.gz -#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139_gene.gff3.gz - -( zcat Ppersica_139_gene.gff3.gz ; echo "###" ; echo "##FASTA" ; zcat Ppersica_139.fa.gz ) > genes.gff - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/rice5/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/rice5/._mRnaAddParent.pl |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/rice5/genes.sh --- a/snpEff_2_1a/scripts/data/rice5/genes.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -#!/bin/sh - -cat ORI/build5_locus.gff3 > genes.gff -cat ORI/build5_genes.gff3 | ./mRnaAddParent.pl >> genes.gff -echo "###" >> genes.gff -echo "##FASTA" >> genes.gff -cat ORI/IRGSPb5.fa >> genes.gff |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl --- a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,28 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# Add 'Parent' option in mRNA lines -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -while( $l = <STDIN> ) { - chomp $l; - @t = split /\t/,$l; - - $type = $t[2]; - - # Is it an mRNA? - if( $type eq 'mRNA' ) { - # Parse ID in options - $opts = $t[8]; - if( $opts =~ /ID=(.*?)-\d+;/ ) { - $pid = $1; - $pid =~ tr/t/g/; - # Add 'Parent' option - $l .= ";Parent=$pid"; - } - } - - print "$l\n"; -} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/distro.sh --- a/snpEff_2_1a/scripts/distro.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,47 +0,0 @@ -#!/bin/sh - -#------------------------------------------------------------------------------ -# Create a zip file for distribution -# Note: Only binary data is included (no raw gene info / genomes) -# -# Pablo Cingolani 2010 -#------------------------------------------------------------------------------ - -VERSION="2_1" -VERSION_REV=$VERSION"a" -DIR=$HOME/snpEff_$VERSION_REV -rm -rvf $DIR -mkdir $DIR - -# Copy core files -cp snpEff.config snpEff.jar $DIR -cp -rvfH galaxy scripts $DIR - -cd $DIR -rm -rvf `find . -name "CVS" -type d` -cd - - -# Create 'core' zip file -cd $HOME -ZIP="snpEff_v"$VERSION_REV"_core.zip" -rm -f $ZIP 2> /dev/null -zip -r $ZIP snpEff_$VERSION_REV -cd - - -# Create ZIP file for each database -for d in `ls data/*/snpEffectPredictor.bin` -do - DIR=`dirname $d` - GEN=`basename $DIR` - - echo $GEN - ZIP="snpEff_v"$VERSION"_"$GEN".zip" - zip -r $ZIP data/$GEN/*.bin -done - -# Look for missing genomes -echo Missing genomes: -ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt -ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt -diff genomes_dirs.txt genomes_bins.txt | grep "^<" - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/download.sh --- a/snpEff_2_1a/scripts/download.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,120 +0,0 @@ -#!/bin/sh -e - -RELEASE=66 - -# mkdir download -cd download - -#--- -# Download -#--- - -# # Download GTF files (annotations) -# wget -r -A "*gtf.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" -# -# # Download FASTA files (reference genomes) -# wget -r -A "*toplevel.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" -# -# # Download CDS sequences -# wget -r -A "*cdna.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" -# -# # Download PROTEIN sequences -# wget -r -A "*.pep.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" - -#--- -# Create directory structure -#--- - -# # Move all downloaded file to this directory -# mv `find ftp.ensembl.org -type f` . - -# # Gene annotations files -# for gtf in *.gtf.gz -# do -# short=`../scripts/file2GenomeName.pl $gtf | cut -f 5` -# echo ANNOTATIONS: $short -# -# mkdir -p data/$short -# cp $gtf data/$short/genes.gtf.gz -# done -# -# # Reference genomes files -# mkdir -p data/genomes -# for fasta in *.dna.toplevel.fa.gz -# do -# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` -# echo REFERENCE: $genome -# -# cp $fasta data/genomes/$genome.fa.gz -# done -# -# # CDS genomes files -# for fasta in *.cdna.all.fa.gz -# do -# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` -# echo CDS: $genome -# -# cp $fasta data/$genome/cds.fa.gz -# done -# -# # Protein seuqence files -# for pep in *.pep.all.fa.gz -# do -# short=`../scripts/file2GenomeName.pl $pep | cut -f 5` -# echo PROTEIN: $short -# -# mkdir -p data/$short -# cp $pep data/$short/protein.fa.gz -# done - -#--- -# Config file entries -#--- - -# for fasta in *.cdna.all.fa.gz -# do -# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 4` -# short=`../scripts/file2GenomeName.pl $fasta | cut -f 5` -# -# # Individual genome entry -# echo -e "$short.genome : $genome" -# echo -e "$short.reference : ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" -# echo -# done - -# Back to parent dir -cd - > /dev/null - -#--- -# Create build queue entries -#--- - -# rm -vf queue_build.txt -# -# # Build from TXT files -# for genes in data/*/genes.txt* -# do -# dir=`dirname $genes` -# genomeName=`basename $dir` -# echo "./scripts/snpEffXL.sh build -v $genomeName" -# done | sort >> queue_build.txt -# -# # Build from GFF2 files -# echo "./scripts/snpEffXL.sh build -v -gff2 amel2" >> queue_build.txt -# -# # Build from GFF3 files -# for genes in `ls data/*/genes.gff* | grep -v amel2` -# do -# dir=`dirname $genes` -# genomeName=`basename $dir` -# echo "./scripts/snpEffXL.sh build -v -gff3 $genomeName" -# done | sort >> queue_build.txt -# -# # Build from GTF22 files -# for genes in data/*/genes.gtf* -# do -# dir=`dirname $genes` -# genomeName=`basename $dir` -# echo "./scripts/snpEffXL.sh build -v -gtf22 $genomeName" -# done | sort >> queue_build.txt - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/fasta2tab.pl --- a/snpEff_2_1a/scripts/fasta2tab.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,32 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------ -# Split a fasta file (create one file per sequence) -# -# -#------------------------------------------------------------------------------ - -use strict; - -#------------------------------------------------------------------------------ -# Main -#------------------------------------------------------------------------------ - -my($seq, $name) = ('', ''); -my($lineNum, $l, $newName); -#--- -# Read fasta file -#--- -for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { - chomp $l; - if( $l =~/^>\s*(.*)\s*$/ ) { - $newName = $1; - if( $seq ne "" ) { print "$name\t$seq\n"; } - # New sequence - $name = $newName; - $seq = ""; - } else { $seq .= $l; } -} - -if( $seq ne "" ) { print "$name\t$seq\n"; } - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/fastaSample.pl --- a/snpEff_2_1a/scripts/fastaSample.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,41 +0,0 @@ -#!/usr/bin/perl - -#--- -# Initialize parameters -#--- -$sampleStart = $ARGV[0]; -$sampleEnd = $ARGV[1]; -if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; } - -$sampleStart--; -$sampleEnd--; -$sampleLen = $sampleEnd - $sampleStart + 1; - -#--- -# Read fasta file -#--- -for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { - if( $l =~/^>/ ) { - # Sample if not empty - if( $seq ne "" ) { - $s = substr( $seq, $sampleStart, $sampleLen); - print "$s\n"; - } - # New sequence - $seq = ""; - } else { - chomp($l); - $seq .= $l; - } -} - -# Sample if not empty -if( $seq ne "" ) { - $s = substr( $seq, $sampleStart, $sampleLen); - print "$s\n"; -} - -$len = length($seq); -print STDERR "Lines: $lineNum\n"; -print STDERR "Sequence size: $len\n"; -print STDERR "Sample size: $sampleLen\n"; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/fastaSplit.pl --- a/snpEff_2_1a/scripts/fastaSplit.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,42 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------ -# Split a fasta file (create one file per sequence) -# -# -#------------------------------------------------------------------------------ - -use strict; - -#------------------------------------------------------------------------------ -# Write fasta file -#------------------------------------------------------------------------------ -sub writeSeq($$) { - my($name, $seq) = @_; - $name = "chr" . $name . ".fa"; - print "Writing to $name\n"; - open OUT, "> $name"; - print OUT $seq; - close OUT; -} - -#------------------------------------------------------------------------------ -# Main -#------------------------------------------------------------------------------ - -my($seq, $name) = ('', ''); -my($lineNum, $l, $newName); -#--- -# Read fasta file -#--- -for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { - if( $l =~/^>\s*(.*?)\s+.*/ ) { - $newName = $1; - if( $seq ne "" ) { writeSeq($name, $seq); } - # New sequence - $name = $newName; - $seq = $l; - } else { $seq .= $l; } -} - -if( $seq ne "" ) { writeSeq($name, $seq); } |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/file2GenomeName.pl --- a/snpEff_2_1a/scripts/file2GenomeName.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# -# Transform file name to genome short name -# -#------------------------------------------------------------------------------- - -$file = $ARGV[0]; -print "$file"; - -$base = `basename $file`; -chomp $base; -print "\t$base"; - -if( $base =~ /(.*?)\.(.*)\..?dna\.(.*)\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } -elsif( $base =~ /(.*?)\.(.*)\.gtf\.gz/ ) { ($gen, $short) = ($1, $2); } -elsif( $base =~ /(.*?)\.(.*)\.pep\.all\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } -$full = "$gen.$short"; -print "\t$full\t$gen\t$short"; - - -print "\n"; - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/filterOutBoringPredictions.sh --- a/snpEff_2_1a/scripts/filterOutBoringPredictions.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -#!/bin/sh - -# Remove some (boring) predictions -grep -v DOWNSTREAM \ - | grep -v UPSTREAM \ - | grep -v INTRON \ - | grep -v UTR_5_PRIME \ - | grep -v UTR_3_PRIME \ - | grep -v INTERGENIC \ - | grep -v " SYNONYMOUS_CODING" \ - | grep -v WITHIN_NON_CODING_GENE |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh --- a/snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -#!/bin/sh - -# Keep interesting predictions -java -jar $HOME/tools/VcfEtc.jar filter \ - "( EFF =~ 'NON_SYN' ) | ( EFF =~ 'CODON') | ( EFF =~ 'SPLICE') | ( EFF =~ 'STOP') | ( EFF =~ 'START') | ( EFF =~ 'FRAME') | ( EFF =~ 'LOST') | ( EFF =~ 'DELETED' )" \ - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/genesTxtColumnNames.sh --- a/snpEff_2_1a/scripts/genesTxtColumnNames.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,33 +0,0 @@ -#!/bin/sh - -#------------------------------------------------------------------------------- -# Convert the gene names in order to be used in an R script -# -# Usage: cat snpEff_genes.txt | ./scripts/genesTxtColumnNames.sh > genes.txt -# -# Once in R, you can: -# - Load this table: -# data <- read.csv("genes.txt", sep= "\t", header=TRUE); -# -# - Access the data: -# data$countINTRON -# -# - Add missing or empty columns: -# if( is.null(data$countINTRON ) { data$countINTRON <- 0 * (1:length(data$geneId) ); } -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -cat \ - | grep -v "^# The following"\ - | sed "s/Bases affected (/bases/g" \ - | sed "s/Length (/len/g" \ - | sed "s/Count (/count/g" \ - | sed "s/Total score (/score/g" \ - | sed "s/)//g" \ - | sed "s/#GeneId/geneId/" \ - | sed "s/GeneName/geneName/" \ - | sed "s/BioType/bioType/" \ - | sed "s/_PRIME//g" \ - | sed "s/SPLICE_SITE_//g" \ - | sed "s/SYNONYMOUS_CODING/SYN/g" \ |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/hist.pl --- a/snpEff_2_1a/scripts/hist.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,88 +0,0 @@ -#!/usr/bin/perl -#------------------------------------------------------------------------------- -# -# Plot a histogram (using R) -# Data is feed as a 1 column of numbers -# -# Note: Any line that does not match a numeric regular expression, is filtered out). -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- -# Main -#------------------------------------------------------------------------------- - -# Parse command line option (file base name) -$base = 'hist'; -if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } - -$pngFile = "$base.png"; -$txtFile = "$base.txt"; - -# Read STDIN and create an R vector -open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; -print TXT "x\n"; -for( $ln = 0 ; $l = <STDIN> ; ) { - chomp $l; - - # Does the string contain exactly one number? (can be float) - if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } -} -close TXT; - -#--- -# Create an R program, save histogram plot as PNG image -#--- - -open R, "| R --vanilla --slave " or die "Cannot open R program\n"; -print R <<EOF; - -histDens <- function( x, title, q=1.0, breaks = 30 ) { - # Show only this part of the data - xmin <- quantile( x, 1-q ) - xmax <- quantile( x, q ) - data <- x[ (x >= xmin) & (x <= xmax) ]; - - dens <- density(data) - - h <- hist(data, main=title, xlab = "data", ylab = "Frequency", freq = T, breaks=breaks); - - # Adjust density height to 'frecuency' - dens\$y <- max(h\$counts) * dens\$y/max(dens\$y) - lines(dens, col='red') - - # Mean & median calculated over the whola data - abline( v=mean(x), col='blue', lty=2, lwd=2); - abline( v=median(x), col='green', lty=2, lwd=2); - - legend("topright",c("Mean","Median"),lty=c(1,1),col=c("blue","green")) - -} - -png('$pngFile', width = 1024, height = 1024); -par( mfrow=c(2,1) ); - -data <- read.csv("$txtFile", sep='\\t', header = TRUE); -x <- data\$x - -histDens( x, "Histogram: All data", 1.0 ); -histDens( x, "Histogram: Quantile [2% - 98%]", 0.98 ); - -print( summary( x ) ) - -dev.off(); -quit( save='no' ) -EOF - -close R; - -#--- -# Show figure -#--- - -$os = `uname`; -$show = "eog"; -if( $os =~ "Darwin" ) { $show = "open"; } -`$show $pngFile`; - |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/joinSnpEff.pl --- a/snpEff_2_1a/scripts/joinSnpEff.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,125 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------ -# -# Mark snps as X1, X2 or 'Both' -# -#------------------------------------------------------------------------------ - -use strict; - -my($debug) = 0; - -#------------------------------------------------------------------------------ -# Read a file and index lines by SNP -#------------------------------------------------------------------------------ -sub readSnps($) { - my($file) = (@_); - my($l, %snps); - - open SNP, $file || die "Cannot open file '$file'\n"; - while( $l = <SNP> ) { - my($chr, $pos, $ref, $var) = split /\t/, $l; - my($snp) = "$chr:$pos\_$ref/$var"; - $snps{$snp} .= $l; - } - close SNP; - return %snps; -} - -#------------------------------------------------------------------------------ -# Print SNP info and quals -#------------------------------------------------------------------------------ -sub printLine($$$$) { - my($snp, $lines, $quals, $q) = (@_); - my($line, @lines); - (@lines) = split '\n', $lines; - foreach $line ( @lines ) { - my($l) = replaceSnpQ($line, $q); - print "$l\t$quals\n"; - } -} - -#------------------------------------------------------------------------------ -# Parse snp quality parameter -#------------------------------------------------------------------------------ -sub parseSnpQ($) { - my($l) = @_; - my(@t); - (@t) = split /\t/,$l; - return $t[6]; -} - -#------------------------------------------------------------------------------ -# Replace a quality -#------------------------------------------------------------------------------ -sub replaceSnpQ($$) { - my($line, $q) = @_; - my(@t); - (@t) = split /\t/, $line; - $t[1] = $q; - return join("\t", @t); -} - -#------------------------------------------------------------------------------ -# Main -#------------------------------------------------------------------------------ -# Read arguments -my(@file); -(@file) = @ARGV; -if( $#file <= 0 ) { die "Usage: ./joinSnpEff.pl tag1 file1 tag2 file2 ... tagN fileN\n"; } - -# Parse arguments -print STDERR "Reading files:\n"; -my($i, $j, $file, $tag, $snp, @snpsAll, %snps, @tags); -for( $i=0 , $j=0 ; $i < $#ARGV ; $i+=2, $j++ ) { - # Read tag - $tags[$j] = $tag = $ARGV[$i]; - - # Read file - $file = $ARGV[$i+1]; - if( $file eq '' ) { die "Missing file for tag '$tag'\n"; } - print STDERR "\tTags[$j]: $tag\t'$file'\n"; - %snps = readSnps($file); - - # Add all snps - foreach $snp ( keys %snps ) { $snpsAll[$j]->{$snp} = $snps{$snp}; } -} - -#--- -# Print SNPS -#--- -my($snp, %done, %snpsi); -my($j, $jj); -$i = 0; -print STDERR "Joining SNP from all files\n"; -for( $i=0 ; $i <= $#tags ; $i++ ) { # For all tags - print "TAG:\ttags[$i] = '$tags[$i]'\n" if $debug; - my($uniq, $shared) = (0, 0); - %snpsi = %{$snpsAll[$i]}; - foreach $snp (sort keys %snpsi) { # For all snps... - if( ! $done{$snp} ) { # Not done yet? - - # Get qualities from all SNPs - my($quals, $qSum, $qCount) = ("", 0, 0); - my($all) = "ALL "; - for( $j=0, $jj=1 ; $j <= $#snpsAll ; $j++ , $jj++ ) { - if( exists $snpsAll[$j]{$snp} ) { - my($q) = parseSnpQ($snpsAll[$j]->{$snp}); - $quals .= "$tags[$j]:$q "; - $qSum += $q; - $qCount++; - } else { $all = ""; } - } - - if( $qCount <= 1 ) { $uniq++; } # Count unique SNPs for this file - else { $shared++; } - - $done{$snp} = 1; - my($qAvg) = ( $qCount > 0 ? int($qSum/$qCount) : 0); - printLine($snp, $snpsi{$snp}, "$all $quals", $qAvg); - } else { $shared++; } - } - print STDERR "\tTags[$i]: $tags[$i]\tUnique / Shared snps: $uniq / $shared\n"; -} - |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/nOutOfM.pl --- a/snpEff_2_1a/scripts/nOutOfM.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# -# Keep variants present in N out of M samples (multi-sample VCF file) -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/promoterSequences.sh --- a/snpEff_2_1a/scripts/promoterSequences.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff/ - -java -Xmx3G \ - -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ - ca.mcgill.mcb.pcingola.PromoterSequences \ - $* |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/proteinFasta2NM.pl --- a/snpEff_2_1a/scripts/proteinFasta2NM.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,45 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# -# Convert fasta headers from protein ID (NP_XXXX) into transcript ID NM_XXXX -# -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -# Parse command line arguments -$refLink = $ARGV[0]; -die "Usage: cat file.fasta | ./proteinFasta2NM.pl refLink.txt > protein_NM.fasta" if $refLink eq ''; - -# Read refLink file -open RL, $refLink or die "Cannot opne file '$refLink'\n"; -while( <RL> ) { - chomp; - @t = split /\t/; - ($nm, $np) = ($t[2], $t[3]); - - if( $np ne '' ) { - if( $trId{$np} ne '' ) { print STDERR "Error: Non empty entry '$np' = $trId{$np}\n"; } - else { $trId{$np} = $nm; } - } -} - -# Read fasta file -while( <STDIN> ) { - chomp; - - if( /^>(.*)/ ) { # Header? => change form protein NP_XXX to transcript NM_XXXX - # Get NM_ field - @t = split /\|/; - $np = $t[3]; - - # Remove anything after the dot - if( $np =~ /(.*)\./ ) { $np = $1; } - - # Found a transcript ID? - if( $trId{$np} ne '' ) { print ">$trId{$np}\n"; } - else { print "$l\n"; } - } else { print "$_\n"; } # Show line -} - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/qqplot.pl --- a/snpEff_2_1a/scripts/qqplot.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,80 +0,0 @@ -#!/usr/bin/perl -#------------------------------------------------------------------------------- -# -# Plot a QQ plot (using R) -# Data is feed as a 1 column of numbers -# -# Note: Any line that does not match a numeric regular expression, is filtered out). -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- -# Main -#------------------------------------------------------------------------------- - -# Parse command line option (file base name) -$base = 'QQ-plot'; -if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } - -$pngFile = "$base.png"; -$txtFile = "$base.txt"; - -# Read STDIN and create an R vector -open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; -print TXT "x\n"; -for( $ln = 0 ; $l = <STDIN> ; ) { - chomp $l; - - # Does the string contain exactly one number? (can be float) - if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } -} -close TXT; - -#--- -# Create an R program, save QQ-plot as PNG image -#--- - -open R, "| R --vanilla --slave " or die "Cannot open R program\n"; -print R <<EOF; - -qqplot <- function( x, title ) { - keep <- (x > 0) & (x <= 1) & ( ! is.na(x) ); - x <- x[keep] - s <- sort(x); - ly <- -log10(s); - - n <- length(s); - lx <- -log10( (1:n) / (n+1) ) - - # Show auto range - #par( mfrow=c(2,1) ); - #plot( lx, ly, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); - #abline( 0 , 1 , col='red'); - - # Show full range in both plots - range <- c(0 , max(lx, ly) ); - plot( lx, ly, xlim=range, ylim=range, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); - abline( 0 , 1 , col='red'); -} - -png('$pngFile', width = 1024, height = 1024); - -data <- read.csv("$txtFile", sep='\t', header = TRUE); -qqplot( data\$x, "$base" ); - -dev.off(); -quit( save='no' ) -EOF - -close R; - -#--- -# Show figure -#--- - -$os = `uname`; -$show = "eog"; -if( $os =~ "Darwin" ) { $show = "open"; } -`$show $pngFile`; - |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue.pl --- a/snpEff_2_1a/scripts/queue.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,127 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# Simple queue management program -# Attempts to keep 'numProc' processes running at the same time -# -# Proceses are defined in a file (one line per process) -# -# Every executed process creates two files: 'pid.stdout' and 'pid.stderr' where -# pid is the process ID. The files contain STDOUT and STDERR for that process. -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -use strict; -use POSIX; - - -my($uptimeCmd) = "/usr/bin/uptime"; # Uptime command -my($maxUptime); -$| = 1; # Don't use buffers for STDIN/STDOUT - -#------------------------------------------------------------------------------- -# Should a new process be run? -# Check some conditions before trying to run the next process -#------------------------------------------------------------------------------- -sub shouldRun() { - if( $maxUptime < 0 ) { return 1; } # Always true if $maxUptime is negative - my($utRes) = `$uptimeCmd`; - my($ut) = 0; - if( $utRes =~ /load average:\s+(\d+\.\d+),/ ) { $ut = $1; } - return $ut < $maxUptime; -} - -#------------------------------------------------------------------------------- -# Print something 'printLog' style -#------------------------------------------------------------------------------- -sub printLog($) { - my($str) = @_; - my($now) = strftime "%Y-%m-%d %H:%M:%S", localtime; - print "$now\t$str\n"; -} - -#------------------------------------------------------------------------------- -# Main -#------------------------------------------------------------------------------- -# Usage: queue numProc File -my($maxNumProc, $sleepTime, $file); -($maxNumProc, $maxUptime, $sleepTime, $file) = @ARGV; -if( $file eq '' ) { - print "Usage: queue.pl maxNumProc maxUptime sleepTime file\n"; - print "Where:\n"; - print "\tnumProc Number of simultaneous processes\n"; - print "\tmaxUptime Maximum allowed uptime (otherwise, pause before launching the next process). Negative means don't care.\n"; - print "\tsleepTime Number of seconds to sleep after running a process (zero means no sleep)\n"; - print "\tfile File containing all commands to be executed (one per line)\n"; - exit(10); -} - -#--- -# Read file and launch processes -#--- -my($cmd); -my($startTime) = time(); -my($numProc) = 0; -open BATCH, $file; -while( $cmd = <BATCH> ) { - chomp $cmd; - - # Can we launch more processes? - if( $numProc < $maxNumProc ) { - - my( $run ) = 0; - - do { - # Should the next process run now? (don't run if CPU is too high) - if( shouldRun() ) { - my $retFork = fork(); - $run = 1; - - if( $retFork == 0 ) { # Child process - # Redirect STDOUT and STDERR to files - open STDOUT, '>', "$$.stdout" or die "Can't redirect STDOUT (PID=$$): $!"; - open STDERR, '>', "$$.stderr" or die "Can't redirect STDERR (PID=$$): $!"; - exec($cmd); - } elsif ($retFork == '' ) { # Error launching process - print STDERR "Error launching process:\t'$cmd'\n"; - } else { - printLog("Executing (PID=$retFork):\t'$cmd'"); - $numProc++; - } - } else { printLog("No running"); } - - # Sleep before next process - if( $sleepTime > 0 ) { - printLog "Sleep $sleepTime seconds"; - sleep($sleepTime); - } - } while( ! $run ); - } - - # Number of processes exceded? => Wait until one finishes - if( $numProc >= $maxNumProc ) { - # Wait for processes to die - my $deadPid = wait(); - printLog "Process PID=$deadPid finished."; - $numProc--; - if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } - } -} - -#--- -# Done, wait for the remining processes to die -#--- -my($deadPid); -while( ($deadPid = wait()) >= 0 ) { # Wait for processes to die - $numProc--; - my($now) = localtime(); - printLog "Process PID=$deadPid finished."; - if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } -} - -my($elapsed) = time() - $startTime; -print "All processes finished.\nElapsed time $elapsed seconds.\n"; - -close BATCH; - |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_build.sh --- a/snpEff_2_1a/scripts/queue_build.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#!/bin/sh - -./scripts/queue.pl 22 24 15 ./scripts/queue_build.txt |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_build.txt --- a/snpEff_2_1a/scripts/queue_build.txt Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,387 +0,0 @@\n-./scripts/snpEffXL.sh build -v anoCar1.0.60\n-./scripts/snpEffXL.sh build -v btau4.0.59\n-./scripts/snpEffXL.sh build -v btau4.0.60\n-./scripts/snpEffXL.sh build -v bushBaby1.60\n-./scripts/snpEffXL.sh build -v calJac3.2.1.60\n-./scripts/snpEffXL.sh build -v canFam2.59\n-./scripts/snpEffXL.sh build -v canFam2.60\n-./scripts/snpEffXL.sh build -v cat1.60\n-./scripts/snpEffXL.sh build -v cavPor3.60\n-./scripts/snpEffXL.sh build -v ce.WS210.60\n-./scripts/snpEffXL.sh build -v chimp2.1.59\n-./scripts/snpEffXL.sh build -v chimp2.1.60\n-./scripts/snpEffXL.sh build -v choHof1.60\n-./scripts/snpEffXL.sh build -v cInt2.60\n-./scripts/snpEffXL.sh build -v cSav2.0.60\n-./scripts/snpEffXL.sh build -v danRer8.59\n-./scripts/snpEffXL.sh build -v danRer9.60\n-./scripts/snpEffXL.sh build -v dasNov2.60\n-./scripts/snpEffXL.sh build -v dipOrd1.60\n-./scripts/snpEffXL.sh build -v dm5.25.59\n-./scripts/snpEffXL.sh build -v dm5.25.60\n-./scripts/snpEffXL.sh build -v equCab2.60\n-./scripts/snpEffXL.sh build -v eriEur1.60\n-./scripts/snpEffXL.sh build -v fugu4.60\n-./scripts/snpEffXL.sh build -v gacu1.60\n-./scripts/snpEffXL.sh build -v ggallus2.59\n-./scripts/snpEffXL.sh build -v ggallus2.60\n-./scripts/snpEffXL.sh build -v gorGor3.60\n-./scripts/snpEffXL.sh build -v hg19\n-./scripts/snpEffXL.sh build -v hg37.59\n-./scripts/snpEffXL.sh build -v hg37.60\n-./scripts/snpEffXL.sh build -v hiv\n-./scripts/snpEffXL.sh build -v loxAfr3.60\n-./scripts/snpEffXL.sh build -v medaka1.60\n-./scripts/snpEffXL.sh build -v meug1.0.60\n-./scripts/snpEffXL.sh build -v micMur1.60\n-./scripts/snpEffXL.sh build -v mm37\n-./scripts/snpEffXL.sh build -v mm37.59\n-./scripts/snpEffXL.sh build -v mm37.60\n-./scripts/snpEffXL.sh build -v mmul1.60\n-./scripts/snpEffXL.sh build -v monDom5.60\n-./scripts/snpEffXL.sh build -v myoLuc1.60\n-./scripts/snpEffXL.sh build -v oana5.60\n-./scripts/snpEffXL.sh build -v ochPri2.60\n-./scripts/snpEffXL.sh build -v oryCun2.60\n-./scripts/snpEffXL.sh build -v ppyg2.60\n-./scripts/snpEffXL.sh build -v proCap1.60\n-./scripts/snpEffXL.sh build -v pteVam1.60\n-./scripts/snpEffXL.sh build -v rat3.4.59\n-./scripts/snpEffXL.sh build -v rat3.4.60\n-./scripts/snpEffXL.sh build -v sacCer2\n-./scripts/snpEffXL.sh build -v sacCer2.59\n-./scripts/snpEffXL.sh build -v sacCer2.60\n-./scripts/snpEffXL.sh build -v SIVmac239\n-./scripts/snpEffXL.sh build -v sorAra1.60\n-./scripts/snpEffXL.sh build -v speTri1.60\n-./scripts/snpEffXL.sh build -v sScrofa9.60\n-./scripts/snpEffXL.sh build -v taeGut3.2.4.60\n-./scripts/snpEffXL.sh build -v tarSyr1.60\n-./scripts/snpEffXL.sh build -v tenrec1.60\n-./scripts/snpEffXL.sh build -v testCase\n-./scripts/snpEffXL.sh build -v tetraodon8.60\n-./scripts/snpEffXL.sh build -v tupBel1.60\n-./scripts/snpEffXL.sh build -v turTru1.60\n-./scripts/snpEffXL.sh build -v vicPac1.60\n-./scripts/snpEffXL.sh build -v xtrop4.1.60\n-./scripts/snpEffXL.sh build -v -gff2 amel2\n-./scripts/snpEffXL.sh build -v -gff3 agam\n-./scripts/snpEffXL.sh build -v -gff3 alyrata107\n-./scripts/snpEffXL.sh build -v -gff3 aquiCoer\n-./scripts/snpEffXL.sh build -v -gff3 athaliana130\n-./scripts/snpEffXL.sh build -v -gff3 athalianaTair10\n-./scripts/snpEffXL.sh build -v -gff3 athalianaTair9\n-./scripts/snpEffXL.sh build -v -gff3 cAlbicansv21\n-./scripts/snpEffXL.sh build -v -gff3 c_briggsae_WS230\n-./scripts/snpEffXL.sh build -v -gff3 ce.WS201\n-./scripts/snpEffXL.sh build -v -gff3 dm5.12\n-./scripts/snpEffXL.sh build -v -gff3 dm5.22\n-./scripts/snpEffXL.sh build -v -gff3 dm5.30\n-./scripts/snpEffXL.sh build -v -gff3 dm5.31\n-./scripts/snpEffXL.sh build -v -gff3 dm5.32\n-./scripts/snpEffXL.sh build -v -gff3 dm5.34\n-./scripts/snpEffXL.sh build -v -gff3 dm5.40\n-./scripts/snpEffXL.sh build -v -gff3 dm5.42\n-./scripts/snpEffXL.sh build -v -gff3 gmax1.09\n-./scripts/snpEffXL.sh build -v -gff3 gmax1.09v8\n-./scripts/snpEffXL.sh build -v -gff3 kw1407.2012\n-./scripts/snpEffXL.sh build -v -gff3 kw1407.2012\n-./scripts/snpEffXL.sh build -v -gff3 maizeZmB73\n-./scripts/snpEffXL.sh build -v -gff3 mmm.2012\n-./scripts/snpEffXL.sh build -v'..b'uild -v -gtf22 pteVam1.63\n-./scripts/snpEffXL.sh build -v -gtf22 pteVam1.64\n-./scripts/snpEffXL.sh build -v -gtf22 pteVam1.65\n-./scripts/snpEffXL.sh build -v -gtf22 pteVam1.66\n-./scripts/snpEffXL.sh build -v -gtf22 rat3.4.61\n-./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.63\n-./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.64\n-./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.65\n-./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.66\n-./scripts/snpEffXL.sh build -v -gtf22 sacCer2.61\n-./scripts/snpEffXL.sh build -v -gtf22 sorAra1.61\n-./scripts/snpEffXL.sh build -v -gtf22 speTri1.61\n-./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.63\n-./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.64\n-./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.65\n-./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.66\n-./scripts/snpEffXL.sh build -v -gtf22 sScrofa9.61\n-./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.63\n-./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.64\n-./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.65\n-./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.66\n-./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.61\n-./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.63\n-./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.64\n-./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.65\n-./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.66\n-./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.61\n-./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.63\n-./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.64\n-./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.65\n-./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.66\n-./scripts/snpEffXL.sh build -v -gtf22 tenrec1.61\n-./scripts/snpEffXL.sh build -v -gtf22 TENREC.63\n-./scripts/snpEffXL.sh build -v -gtf22 TENREC.64\n-./scripts/snpEffXL.sh build -v -gtf22 TENREC.65\n-./scripts/snpEffXL.sh build -v -gtf22 TENREC.66\n-./scripts/snpEffXL.sh build -v -gtf22 test_ENSG00000158062\n-./scripts/snpEffXL.sh build -v -gtf22 testHg3763ChrY\n-./scripts/snpEffXL.sh build -v -gtf22 tetraodon8.61\n-./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.63\n-./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.64\n-./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.65\n-./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.66\n-./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.63\n-./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.64\n-./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.65\n-./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.66\n-./scripts/snpEffXL.sh build -v -gtf22 tupBel1.61\n-./scripts/snpEffXL.sh build -v -gtf22 turkey.UMD2.61\n-./scripts/snpEffXL.sh build -v -gtf22 turTru1.61\n-./scripts/snpEffXL.sh build -v -gtf22 turTru1.63\n-./scripts/snpEffXL.sh build -v -gtf22 turTru1.64\n-./scripts/snpEffXL.sh build -v -gtf22 turTru1.65\n-./scripts/snpEffXL.sh build -v -gtf22 turTru1.66\n-./scripts/snpEffXL.sh build -v -gtf22 UMD2.63\n-./scripts/snpEffXL.sh build -v -gtf22 UMD2.64\n-./scripts/snpEffXL.sh build -v -gtf22 UMD2.65\n-./scripts/snpEffXL.sh build -v -gtf22 UMD2.66\n-./scripts/snpEffXL.sh build -v -gtf22 UMD3_1\n-./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.64\n-./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.65\n-./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.66\n-./scripts/snpEffXL.sh build -v -gtf22 vicPac1.61\n-./scripts/snpEffXL.sh build -v -gtf22 vicPac1.63\n-./scripts/snpEffXL.sh build -v -gtf22 vicPac1.64\n-./scripts/snpEffXL.sh build -v -gtf22 vicPac1.65\n-./scripts/snpEffXL.sh build -v -gtf22 vicPac1.66\n-./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.63\n-./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.64\n-./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.65\n-./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.66\n-./scripts/snpEffXL.sh build -v -gtf22 WS220.63\n-./scripts/snpEffXL.sh build -v -gtf22 WS220.64\n-./scripts/snpEffXL.sh build -v -gtf22 WS220.65\n-./scripts/snpEffXL.sh build -v -gtf22 WS220.66\n-./scripts/snpEffXL.sh build -v -gtf22 xtrop4.1.61\n-./scripts/snpEffXL.sh build -v -gtf22 Zv9.63\n-./scripts/snpEffXL.sh build -v -gtf22 Zv9.64\n-./scripts/snpEffXL.sh build -v -gtf22 Zv9.65\n-./scripts/snpEffXL.sh build -v -gtf22 Zv9.66\n' |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_build_regulation.txt --- a/snpEff_2_1a/scripts/queue_build_regulation.txt Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,73 +0,0 @@ -./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Nuclei GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Kidney GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Liver GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Anterior_Caudate GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Cingulate_Gyrus GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Hippocampus_Middle GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Inferior_Temporal_Lobe GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Mid_Frontal_Lobe GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Substantia_Nigra GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Luminal_Epithelial_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Myoepithelial_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Stem_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_vHMEC GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD15_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD19_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Cultured_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD3_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Memory_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Naive_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD56_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Naive_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Colonic_Mucosa GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Duodenum_Mucosa GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-I3 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-WA7 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Adrenal_Gland GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Brain GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Heart GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Large GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Small GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Left GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Right GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Left GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Right GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Thymus GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType H1 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType H3K9me3 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType H9 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES48 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES6 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES64 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType IMR90 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType input GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-11a GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-15b GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-18c GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-20b GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_19 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_4 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_6 GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD34_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD56_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Muscle_Satellite_Cultured_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Cortex_Derived GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Pancreatic_Islets GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Penis_Foreskin_Keratinocyte_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Peripheral_Blood_Mononuclear_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Mucosa GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Smooth_Muscle GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Skeletal_Muscle GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Stomach_Smooth_Muscle GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Th17_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType Treg_Primary_Cells GRCh37.64 -./scripts/snpEffXL.sh build -v -onlyReg -cellType uniques GRCh37.64 |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_dump.txt --- a/snpEff_2_1a/scripts/queue_dump.txt Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,137 +0,0 @@ -./scripts/snpEff.sh dump agam > agam.dump -./scripts/snpEff.sh dump ailmel1.61 > ailmel1.61.dump -./scripts/snpEff.sh dump alyrata107 > alyrata107.dump -./scripts/snpEff.sh dump alyrata107 > alyrata107.dump -./scripts/snpEff.sh dump amel2 > amel2.dump -./scripts/snpEff.sh dump anoCar1.0.60 > anoCar1.0.60.dump -./scripts/snpEff.sh dump anoCar2.0.61 > anoCar2.0.61.dump -./scripts/snpEff.sh dump aquiCoer > aquiCoer.dump -./scripts/snpEff.sh dump athaliana130 > athaliana130.dump -./scripts/snpEff.sh dump btau4.0.59 > btau4.0.59.dump -./scripts/snpEff.sh dump btau4.0.60 > btau4.0.60.dump -./scripts/snpEff.sh dump btau4.0.61 > btau4.0.61.dump -./scripts/snpEff.sh dump bushBaby1.60 > bushBaby1.60.dump -./scripts/snpEff.sh dump bushBaby1.61 > bushBaby1.61.dump -./scripts/snpEff.sh dump calJac3.2.1.60 > calJac3.2.1.60.dump -./scripts/snpEff.sh dump calJac3.2.1.61 > calJac3.2.1.61.dump -./scripts/snpEff.sh dump canFam2.59 > canFam2.59.dump -./scripts/snpEff.sh dump canFam2.60 > canFam2.60.dump -./scripts/snpEff.sh dump canFam2.61 > canFam2.61.dump -./scripts/snpEff.sh dump cat1.60 > cat1.60.dump -./scripts/snpEff.sh dump cat1.61 > cat1.61.dump -./scripts/snpEff.sh dump cavPor3.60 > cavPor3.60.dump -./scripts/snpEff.sh dump cavPor3.61 > cavPor3.61.dump -./scripts/snpEff.sh dump ce.WS210.60 > ce.WS210.60.dump -./scripts/snpEff.sh dump ce.WS220.61 > ce.WS220.61.dump -./scripts/snpEff.sh dump chimp2.1.59 > chimp2.1.59.dump -./scripts/snpEff.sh dump chimp2.1.60 > chimp2.1.60.dump -./scripts/snpEff.sh dump chimp2.1.61 > chimp2.1.61.dump -./scripts/snpEff.sh dump choHof1.60 > choHof1.60.dump -./scripts/snpEff.sh dump choHof1.61 > choHof1.61.dump -./scripts/snpEff.sh dump cInt2.60 > cInt2.60.dump -./scripts/snpEff.sh dump cInt2.61 > cInt2.61.dump -./scripts/snpEff.sh dump cSav2.0.60 > cSav2.0.60.dump -./scripts/snpEff.sh dump cSav2.0.61 > cSav2.0.61.dump -./scripts/snpEff.sh dump danRer6 > danRer6.dump -./scripts/snpEff.sh dump danRer8.59 > danRer8.59.dump -./scripts/snpEff.sh dump danRer9.60 > danRer9.60.dump -./scripts/snpEff.sh dump danRer9.61 > danRer9.61.dump -./scripts/snpEff.sh dump dasNov2.60 > dasNov2.60.dump -./scripts/snpEff.sh dump dasNov2.61 > dasNov2.61.dump -./scripts/snpEff.sh dump dipOrd1.60 > dipOrd1.60.dump -./scripts/snpEff.sh dump dipOrd1.61 > dipOrd1.61.dump -./scripts/snpEff.sh dump dm5.12 > dm5.12.dump -./scripts/snpEff.sh dump dm5.22 > dm5.22.dump -./scripts/snpEff.sh dump dm5.25.59 > dm5.25.59.dump -./scripts/snpEff.sh dump dm5.25.60 > dm5.25.60.dump -./scripts/snpEff.sh dump dm5.25.61 > dm5.25.61.dump -./scripts/snpEff.sh dump dm5.30 > dm5.30.dump -./scripts/snpEff.sh dump dm5.31 > dm5.31.dump -./scripts/snpEff.sh dump dm5.32 > dm5.32.dump -./scripts/snpEff.sh dump dm5.34 > dm5.34.dump -./scripts/snpEff.sh dump equCab2.60 > equCab2.60.dump -./scripts/snpEff.sh dump equCab2.61 > equCab2.61.dump -./scripts/snpEff.sh dump eriEur1.60 > eriEur1.60.dump -./scripts/snpEff.sh dump eriEur1.61 > eriEur1.61.dump -./scripts/snpEff.sh dump fugu4.60 > fugu4.60.dump -./scripts/snpEff.sh dump fugu4.61 > fugu4.61.dump -./scripts/snpEff.sh dump gacu1.60 > gacu1.60.dump -./scripts/snpEff.sh dump gacu1.61 > gacu1.61.dump -./scripts/snpEff.sh dump ggallus2.59 > ggallus2.59.dump -./scripts/snpEff.sh dump ggallus2.60 > ggallus2.60.dump -./scripts/snpEff.sh dump ggallus2.61 > ggallus2.61.dump -./scripts/snpEff.sh dump gorGor3.60 > gorGor3.60.dump -./scripts/snpEff.sh dump gorGor3.61 > gorGor3.61.dump -./scripts/snpEff.sh dump hg36.54 > hg36.54.dump -./scripts/snpEff.sh dump hg37.59 > hg37.59.dump -./scripts/snpEff.sh dump hg37.60 > hg37.60.dump -./scripts/snpEff.sh dump hg37.61 > hg37.61.dump -./scripts/snpEff.sh dump hg37 > hg37.dump -./scripts/snpEff.sh dump hiv > hiv.dump -./scripts/snpEff.sh dump loxAfr3.60 > loxAfr3.60.dump -./scripts/snpEff.sh dump loxAfr3.61 > loxAfr3.61.dump -./scripts/snpEff.sh dump medaka1.60 > medaka1.60.dump -./scripts/snpEff.sh dump medaka1.61 > medaka1.61.dump -./scripts/snpEff.sh dump meug1.0.60 > meug1.0.60.dump -./scripts/snpEff.sh dump meug1.0.61 > meug1.0.61.dump -./scripts/snpEff.sh dump micMur1.60 > micMur1.60.dump -./scripts/snpEff.sh dump micMur1.61 > micMur1.61.dump -./scripts/snpEff.sh dump mm37.59 > mm37.59.dump -./scripts/snpEff.sh dump mm37.60 > mm37.60.dump -./scripts/snpEff.sh dump mm37.61 > mm37.61.dump -./scripts/snpEff.sh dump mm37 > mm37.dump -./scripts/snpEff.sh dump mmul1.60 > mmul1.60.dump -./scripts/snpEff.sh dump mmul1.61 > mmul1.61.dump -./scripts/snpEff.sh dump monDom5.60 > monDom5.60.dump -./scripts/snpEff.sh dump monDom5.61 > monDom5.61.dump -./scripts/snpEff.sh dump myoLuc1.60 > myoLuc1.60.dump -./scripts/snpEff.sh dump myoLuc1.61 > myoLuc1.61.dump -./scripts/snpEff.sh dump oana5.60 > oana5.60.dump -./scripts/snpEff.sh dump oana5.61 > oana5.61.dump -./scripts/snpEff.sh dump ochPri2.60 > ochPri2.60.dump -./scripts/snpEff.sh dump ochPri2.61 > ochPri2.61.dump -./scripts/snpEff.sh dump oryCun2.60 > oryCun2.60.dump -./scripts/snpEff.sh dump oryCun2.61 > oryCun2.61.dump -./scripts/snpEff.sh dump paeru.PA01 > paeru.PA01.dump -./scripts/snpEff.sh dump paeru.PA14 > paeru.PA14.dump -./scripts/snpEff.sh dump pfluo.SBW25.NC_009444 > pfluo.SBW25.NC_009444.dump -./scripts/snpEff.sh dump pfluo.SBW25.NC_012660 > pfluo.SBW25.NC_012660.dump -./scripts/snpEff.sh dump ppyg2.60 > ppyg2.60.dump -./scripts/snpEff.sh dump ppyg2.61 > ppyg2.61.dump -./scripts/snpEff.sh dump proCap1.60 > proCap1.60.dump -./scripts/snpEff.sh dump proCap1.61 > proCap1.61.dump -./scripts/snpEff.sh dump pteVam1.60 > pteVam1.60.dump -./scripts/snpEff.sh dump pteVam1.61 > pteVam1.61.dump -./scripts/snpEff.sh dump rat3.4.59 > rat3.4.59.dump -./scripts/snpEff.sh dump rat3.4.60 > rat3.4.60.dump -./scripts/snpEff.sh dump rat3.4.61 > rat3.4.61.dump -./scripts/snpEff.sh dump sacCer2.59 > sacCer2.59.dump -./scripts/snpEff.sh dump sacCer2.60 > sacCer2.60.dump -./scripts/snpEff.sh dump sacCer2.61 > sacCer2.61.dump -./scripts/snpEff.sh dump sacCer2 > sacCer2.dump -./scripts/snpEff.sh dump SIVmac239 > SIVmac239.dump -./scripts/snpEff.sh dump sorAra1.60 > sorAra1.60.dump -./scripts/snpEff.sh dump sorAra1.61 > sorAra1.61.dump -./scripts/snpEff.sh dump speTri1.60 > speTri1.60.dump -./scripts/snpEff.sh dump speTri1.61 > speTri1.61.dump -./scripts/snpEff.sh dump sScrofa9.60 > sScrofa9.60.dump -./scripts/snpEff.sh dump sScrofa9.61 > sScrofa9.61.dump -./scripts/snpEff.sh dump taeGut3.2.4.60 > taeGut3.2.4.60.dump -./scripts/snpEff.sh dump taeGut3.2.4.61 > taeGut3.2.4.61.dump -./scripts/snpEff.sh dump tarSyr1.60 > tarSyr1.60.dump -./scripts/snpEff.sh dump tarSyr1.61 > tarSyr1.61.dump -./scripts/snpEff.sh dump tenrec1.60 > tenrec1.60.dump -./scripts/snpEff.sh dump tenrec1.61 > tenrec1.61.dump -./scripts/snpEff.sh dump testCase > testCase.dump -./scripts/snpEff.sh dump tetraodon8.60 > tetraodon8.60.dump -./scripts/snpEff.sh dump tetraodon8.61 > tetraodon8.61.dump -./scripts/snpEff.sh dump tupBel1.60 > tupBel1.60.dump -./scripts/snpEff.sh dump tupBel1.61 > tupBel1.61.dump -./scripts/snpEff.sh dump turkey.UMD2.61 > turkey.UMD2.61.dump -./scripts/snpEff.sh dump turTru1.60 > turTru1.60.dump -./scripts/snpEff.sh dump turTru1.61 > turTru1.61.dump -./scripts/snpEff.sh dump vacwr > vacwr.dump -./scripts/snpEff.sh dump vicPac1.60 > vicPac1.60.dump -./scripts/snpEff.sh dump vicPac1.61 > vicPac1.61.dump -./scripts/snpEff.sh dump xtrop4.1.60 > xtrop4.1.60.dump -./scripts/snpEff.sh dump xtrop4.1.61 > xtrop4.1.61.dump |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_test.sh --- a/snpEff_2_1a/scripts/queue_test.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#!/bin/sh - -./scripts/queue.pl 22 24 15 ./scripts/queue_test.txt |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/queue_test.txt --- a/snpEff_2_1a/scripts/queue_test.txt Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,231 +0,0 @@\n-./scripts/snpEffXL.sh cds -v ailmel1.61 data/ailmel1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v ailMel1.63 data/ailMel1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v ailMel1.64 data/ailMel1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v anoCar1.0.60 data/anoCar1.0.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v anoCar2.0.61 data/anoCar2.0.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v AnoCar2.0.63 data/AnoCar2.0.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v AnoCar2.0.64 data/AnoCar2.0.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BDGP5.25.63 data/BDGP5.25.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BDGP5.25.64 data/BDGP5.25.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADD2.63 data/BROADD2.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADD2.64 data/BROADD2.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADO5.63 data/BROADO5.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADO5.64 data/BROADO5.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADS1.63 data/BROADS1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BROADS1.64 data/BROADS1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v btau4.0.59 data/btau4.0.59/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v btau4.0.60 data/btau4.0.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v btau4.0.61 data/btau4.0.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v Btau_4.0.63 data/Btau_4.0.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v bushBaby1.60 data/bushBaby1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v bushBaby1.61 data/bushBaby1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BUSHBABY1.63 data/BUSHBABY1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v BUSHBABY1.64 data/BUSHBABY1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v calJac3.2.1.60 data/calJac3.2.1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v calJac3.2.1.61 data/calJac3.2.1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v canFam2.59 data/canFam2.59/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v canFam2.60 data/canFam2.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v canFam2.61 data/canFam2.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cat1.60 data/cat1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v cat1.61 data/cat1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CAT.63 data/CAT.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CAT.64 data/CAT.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cavPor3.60 data/cavPor3.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v cavPor3.61 data/cavPor3.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cavPor3.63 data/cavPor3.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cavPor3.64 data/cavPor3.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v ce.WS210.60 data/ce.WS210.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v ce.WS220.61 data/ce.WS220.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v chimp2.1.59 data/chimp2.1.59/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v chimp2.1.60 data/chimp2.1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v chimp2.1.61 data/chimp2.1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CHIMP2.1.63 data/CHIMP2.1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CHIMP2.1.64 data/CHIMP2.1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v choHof1.60 data/choHof1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v choHof1.61 data/choHof1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v choHof1.63 data/choHof1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v choHof1.64 data/choHof1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cInt2.60 data/cInt2.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v cInt2.61 data/cInt2.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.63 data/C_jacchus3.2.1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.64 data/C_jacchus3.2.1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v COMMON_SHREW1.63 data/COMMON_SHREW1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v COMMON_SHREW1.64 data/COMMON_SHREW1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v cSav2.0.60 data/cSav2.0.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v cSav2.0.61 data/cSav2.0.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CSAV2.0.63 data/CSAV2.0.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v CSAV2.0.64 data/CSAV2.0.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v danRer8.59 data/danRer8.59/cds.tx'..b'/scripts/snpEffXL.sh cds -v rat3.4.60 data/rat3.4.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v rat3.4.61 data/rat3.4.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v RGSC3.4.63 data/RGSC3.4.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v RGSC3.4.64 data/RGSC3.4.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v sacCer2.59 data/sacCer2.59/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v sacCer2.60 data/sacCer2.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v sacCer2.61 data/sacCer2.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v sacCer2 data/sacCer2/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v sorAra1.60 data/sorAra1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v sorAra1.61 data/sorAra1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v speTri1.60 data/speTri1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v speTri1.61 data/speTri1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v SQUIRREL.63 data/SQUIRREL.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v SQUIRREL.64 data/SQUIRREL.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v sScrofa9.60 data/sScrofa9.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v sScrofa9.61 data/sScrofa9.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v Sscrofa9.63 data/Sscrofa9.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v Sscrofa9.64 data/Sscrofa9.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v taeGut3.2.4.60 data/taeGut3.2.4.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v taeGut3.2.4.61 data/taeGut3.2.4.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v taeGut3.2.4.63 data/taeGut3.2.4.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v taeGut3.2.4.64 data/taeGut3.2.4.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v tarSyr1.60 data/tarSyr1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v tarSyr1.61 data/tarSyr1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v tarSyr1.63 data/tarSyr1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v tarSyr1.64 data/tarSyr1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v tenrec1.60 data/tenrec1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v tenrec1.61 data/tenrec1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TENREC.63 data/TENREC.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TENREC.64 data/TENREC.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v testCase data/testCase/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v tetraodon8.60 data/tetraodon8.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v tetraodon8.61 data/tetraodon8.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TETRAODON8.63 data/TETRAODON8.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TETRAODON8.64 data/TETRAODON8.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TREESHREW.63 data/TREESHREW.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v TREESHREW.64 data/TREESHREW.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v tupBel1.60 data/tupBel1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v tupBel1.61 data/tupBel1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v turkey.UMD2.61 data/turkey.UMD2.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v turTru1.60 data/turTru1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v turTru1.61 data/turTru1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v turTru1.63 data/turTru1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v turTru1.64 data/turTru1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v UMD2.63 data/UMD2.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v UMD2.64 data/UMD2.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v UMD3.1.64 data/UMD3.1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v vicPac1.60 data/vicPac1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v vicPac1.61 data/vicPac1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v vicPac1.63 data/vicPac1.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v vicPac1.64 data/vicPac1.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v WASHUC2.63 data/WASHUC2.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v WASHUC2.64 data/WASHUC2.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v WS220.63 data/WS220.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v WS220.64 data/WS220.64/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v xtrop4.1.60 data/xtrop4.1.60/cds.txt.gz\n-./scripts/snpEffXL.sh cds -v xtrop4.1.61 data/xtrop4.1.61/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v Zv9.63 data/Zv9.63/cds.fa.gz\n-./scripts/snpEffXL.sh cds -v Zv9.64 data/Zv9.64/cds.fa.gz\n' |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/randBedIntervals.pl --- a/snpEff_2_1a/scripts/randBedIntervals.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,36 +0,0 @@ -#!/usr/bin/perl - -# Number of intervals per chromosome -$intsPerChr = 10; - -# Max interval len -$maxLen = 1000; - -# Chromosome length -$len{'chr2L'} = 23299195; -$len{'chr2LHet'} = 373492; -$len{'chr2R'} = 21411048; -$len{'chr2RHet'} = 3329880; -$len{'chr3L'} = 24850358; -$len{'chr3LHet'} = 2587444; -$len{'chr3R'} = 28253873; -$len{'chr3RHet'} = 2548985; -$len{'chr4'} = 1368761; -$len{'chrdmel_mitochondrion_genome'} = 19790; -$len{'chrUextra'} = 29367225; -$len{'chrU'} = 10174655; -$len{'chrX'} = 22703118; -$len{'chrXHet'} = 206671; -$len{'chrYHet'} = 351384; - -foreach $chr ( sort keys %len ) { - $max = $len{$chr} - $maxLen - 1000; - - for( $i=0 ; $i < $intsPerChr ; $i++ ) { - $start = int( rand() * $max ); - $end = int( rand() * $maxLen ) + $start; - - print "$chr\t$start\t$end\n"; - } -} - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/sift2vcf.pl --- a/snpEff_2_1a/scripts/sift2vcf.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,19 +0,0 @@ -#!/usr/bin/perl - - -print "##INFO=<ID=SIFT_SCORE,Number=1,Type=Float,Description=\"SIFT score, 0 = Damaging, 1=Tolerated\">\n"; -print "##INFO=<ID=SIFT_CONS,Number=1,Type=Float,Description=\"SIFT median conservation value, as log2. 0=High confidence, 4.32=Low confidence\">\n"; -print "##INFO=<ID=SIFT_SEQS,Number=1,Type=Integer,Description=\"SIFT number of sequences at position\">\n"; -print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"; - -while( $l = <STDIN> ) { - chomp $l; - ($chr, $coord1, $nt1, $nt2, $score, $median, $seqs_rep) = split /\t/, $l; - - # Trim spaces - if( $seqs_rep =~ /\s(.*)/ ) { $seqs_rep = $1; } - - $coord1++; # Get it in one-based coordinates - - print "$chr\t$coord1\t.\t$nt1\t$nt2\t.\t.\tSIFT_SCORE=$score;SIFT_CONS=$median;SIFT_SEQS=$seqs_rep\n"; -} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/sift2vcf.sh --- a/snpEff_2_1a/scripts/sift2vcf.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,47 +0,0 @@ -#!/bin/sh -e - -SQLITE=$HOME/tools/sqlite3 -SQLITE=sqlite3 -OUT_FILE="sift.txt" -OUT_SORT_FILE="sift.sort.txt" -OUT_VCF="sift.vcf" - -# Download files -for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sqlite.gz Human_CHR17.sqlite.gz Human_CHR18.sqlite.gz Human_CHR19.sqlite.gz Human_CHR2.sqlite.gz Human_CHR20.sqlite.gz Human_CHR21.sqlite.gz Human_CHR22.sqlite.gz Human_CHR3.sqlite.gz Human_CHR4.sqlite.gz Human_CHR5.sqlite.gz Human_CHR6.sqlite.gz Human_CHR7.sqlite.gz Human_CHR8.sqlite.gz Human_CHR9.sqlite.gz Human_CHRX.sqlite.gz Human_CHRY.sqlite.gz Human_Supp.sqlite.gz Human_enst.sqlite.gz -do - url=ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/$f - echo Getting file $url - #wget $url -done - -# Unzip files -for f in Human_CHR*.sqlite.gz -do - echo Decompressing file $f - #gunzip $f -done - -# Dumping data -rm -f $OUT_FILE -for f in Human_CHR*.sqlite -do - echo Dumping Database $f to $OUT_FILE - - TABLES=`$SQLITE $f ".tables" | tr "\n" "\t"` - for t in $TABLES - do - echo " Dumping Table $t" - - $SQLITE $f "select CHR, COORD1, NT1, NT2, SCORE, MEDIAN, SEQS_REP from $t where SCORE != '' AND NT1 != NT2;" \ - | tr "|" "\t" \ - | sed "s/^chr//" \ - >> $OUT_FILE - done -done - -echo Sorting file -sort -k 1 -n -k 2 -n -o $OUT_SORT_FILE $OUT_FILE - -echo Creating VCF -cat $OUT_SORT_FILE | sift2vcf.pl > $OUT_VCF - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/smoothScatter.pl --- a/snpEff_2_1a/scripts/smoothScatter.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,82 +0,0 @@ -#!/usr/bin/perl -#------------------------------------------------------------------------------- -# -# Plot a smooth scatter plot -# Data is feed as two column of numbers -# -# Note: Any line that does not match a numeric regular expression, is filtered out). -# -# Pablo Cingolani -#------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- -# Main -#------------------------------------------------------------------------------- - -# Parse command line option (file base name) -$base = 'smoothScatter'; -if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } - -$pngFile = "$base.png"; -$txtFile = "$base.txt"; - -# Read STDIN and create an R table -open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; -print TXT "x\ty\n"; -for( $ln = 0 ; $l = <STDIN> ; ) { - chomp $l; - ($x, $y) = split /\t/, $l; - - # Does the string contain exactly one number? (can be float) - if(( $x =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) && ( $y =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ )) { print TXT "$x\t$y\n"; } -} -close TXT; - -#--- -# Create an R program, save histogram plot as PNG image -#--- - -open R, "| R --vanilla --slave " or die "Cannot open R program\n"; -print R <<EOF; - -smoothLowess <- function( x, y, title, q=1.0 ) { - # Show only this part of the data - xmin <- quantile( x, 1-q ) - xmax <- quantile( x, q ) - - ymin <- quantile( y, 1-q ) - ymax <- quantile( y, q ) - - keep <- (x >= xmin) & (x <= xmax) & (y >= ymin) & (y <= ymax); - qx <- x[ keep ] - qy <- y[ keep ] - - smoothScatter(qx, qy, main=title, ylab='Y (column 2)', xlab='X (column 1)'); - lines( lowess(qx,qy), col='orange' ); -} - -png('$pngFile', width = 1024, height = 1024); -par( mfrow=c(2,1) ); - -data <- read.csv("$txtFile", sep='\\t', header = TRUE); -x <- data\$x -y <- data\$y - -smoothLowess(x, y, "Smooth scatter plot and Lowess", 1.0); -smoothLowess(x, y, "Smooth scatter plot and Lowess: Quantile [2% - 98%]", 0.98); - -dev.off(); -quit( save='no' ) -EOF - -close R; - -#--- -# Show figure -#--- - -$os = `uname`; -$show = "eog"; -if( $os =~ "Darwin" ) { $show = "open"; } -`$show $pngFile`; - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/snpEff.sh --- a/snpEff_2_1a/scripts/snpEff.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff/ -LIB=$HOME/snpEff/lib - -java -Xmx1G \ - -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ - ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ - $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/snpEffM.sh --- a/snpEff_2_1a/scripts/snpEffM.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff -LIB=$HOME/snpEff/lib - -java -Xmx3G \ - -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ - ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ - $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/snpEffXL.sh --- a/snpEff_2_1a/scripts/snpEffXL.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff/ -LIB=$HOME/snpEff/lib - -java -Xmx20G \ - -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ - ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ - $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/snpSift.sh --- a/snpEff_2_1a/scripts/snpSift.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -#!/bin/sh - -DIR=$HOME/snpEff/ -DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/ -LIB=$HOME/snpEff/lib -LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/ - -# Old library reference: -# -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR:$DIR_SNPSIFT" \ - -java -Xmx1G \ - -classpath "$LIB/charts4j-1.2.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$LIB_SNPSIFT/antlr-3.4-complete.jar:$DIR:$DIR_SNPSIFT" \ - ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \ - $* - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/test.Broad_NS_SYN.sh --- a/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -#!/bin/sh - -REF=GRCh37.66 - -IN_VCF=$HOME/snpEff/1kg/test.Broad_NS_SYN.vcf.gz -OUT_VCF=all.vcf - -# Run SnpEff -./scripts/snpEffXL.sh eff -v -noStats -o vcf $REF $IN_VCF > $OUT_VCF - -# Calculate number of lines -SILENT=`cat $OUT_VCF | grep "SILENT" | wc -l` -MISSENSE=`cat $OUT_VCF | grep "MISSENSE" | wc -l` -NONSENSE=`cat $OUT_VCF | grep "NONSENSE" | wc -l` -SILENT_AND_MISSENSE=`cat $OUT_VCF | grep "SILENT" | grep "MISSENSE" | wc -l` - -PSILENT=`echo "100 * $SILENT/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` -PMISSENSE=`echo "100 * $MISSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` -PNONSENSE=`echo "100 * $NONSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` - -echo -e "Silent :\t$SILENT ($PSILENT %)" -echo -e "Missense :\t$MISSENSE ($PMISSENSE %)" -echo -e "Nonsense :\t$NONSENSE ($PNONSENSE %)" -echo -e "Silent and missense :\t$SILENT_AND_MISSENSE" - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/uniqCount.pl --- a/snpEff_2_1a/scripts/uniqCount.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -#!/usr/bin/perl - -while( $l = <STDIN> ) { - chomp $l; - $count{$l}++; -} - -$tot = 0; -foreach $key ( sort keys %count ) { - print "$count{$key}\t$key\n"; - $tot += $count{$key}; -} -print "$tot\tTotal\n"; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/vcfEffOnePerLine.pl --- a/snpEff_2_1a/scripts/vcfEffOnePerLine.pl Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,53 +0,0 @@ -#!/usr/bin/perl - -#------------------------------------------------------------------------------- -# -# Read a VCF file (via STDIN), split EFF fields from INFO column into many lines -# leaving one line per effect. -# -# Note: In lines having multiple effects, all other information will be -# repeated. Only the 'EFF' field will change. -# -# Pablo Cingolani 2012 -#------------------------------------------------------------------------------- - -$INFO_FIELD_NUM = 7; - -while( $l = <STDIN> ) { - # Show header lines - if( $l =~ /^#/ ) { print $l; } - else { - chomp $l; - - @t = @infos = @effs = (); # Clear arrays - - # Non-header lines: Parse fields - @t = split /\t/, $l; - - # Get INFO column - $info = $t[ $INFO_FIELD_NUM ]; - - # Parse INFO column - @infos = split /;/, $info; - - # Find EFF field - $infStr = ""; - foreach $inf ( @infos ) { - # Is this the EFF field? => Find it and split it - if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; } - else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; } - } - - # Print VCF line - if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line - else { - $pre = ""; - for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; } - - $post = ""; - for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; } - - foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; } - } - } -} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/scripts/vcfSpeedTest.sh --- a/snpEff_2_1a/scripts/vcfSpeedTest.sh Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -#!/bin/sh - -for testNum in 1 2 3 4 -do - ./scripts/snpEffM.sh test $testNum test.1M.vcf > test.1M.out.vcf - echo -done - |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff.config --- a/snpEff_2_1a/snpEff.config Fri Apr 20 11:16:44 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,1160 +0,0 @@\n-\n-#-------------------------------------------------------------------------------\n-#\n-# SnpEff configuration file\n-#\n-#\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tPablo Cingolani\n-#-------------------------------------------------------------------------------\n-\n-#---\n-# Databases are stored here\n-# E.g.: Information for 'hg19' is stored in data_dir/hg19/\n-#\n-# Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory\n-#---\n-data_dir = ~/snpEff/data/\n-\n-#---\n-# Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')\n-#---\n-database_repository = http://downloads.sourceforge.net/project/snpeff/databases\n-\n-#-------------------------------------------------------------------------------\n-# Genomes\n-#\n-# One entry per genome version. \n-#\n-# For genome version 'ZZZ' the entries look like\n-#\tZZZ.genome : Real name for ZZZ (e.g. 'Human')\n-#\tZZZ.reference : [Optional] Comma separated list of URL to site/s where information for building ZZZ database was extracted.\n-#\tZZZ.chrName.codonTable : [Optional] Define codon table used for chromosome 'chrName' (Default: 'codon.Standard')\n-#\n-#-------------------------------------------------------------------------------\n-\n-# Ailuropoda_melanoleuca\n-ailmel1.61.genome : Ailuropoda_melanoleuca\n-\n-# Anopheles_gambiae\n-agam.genome : Anopheles_gambiae\n-agam.reference : http://agambiae.vectorbase.org/GetData/ \n-\n-agam2.6.genome : Anopheles_gambiae\n-agam2.6.reference : http://agambiae.vectorbase.org/GetData/ \n-\n-# Arabidopsis lyrata\n-alyrata107.genome : Arabidopsis_lyrata\n-alyrata107.reference : http://www.phytozome.net/search.php?method=Org_Alyrata\n-\n-alyrata1.genome : Arabidopsis_lyrata\n-alyrata1.reference : http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html\n-\n-# Apis mellifera\n-amel2.genome : Bee\n-amel2.reference : http://beebase.org\n-\n-# Anolis carolinensis genes (AnoCar1.0) (ENSEMBL)\n-anoCar1.0.60.genome : Anolis_carolinensis\n-anoCar2.0.61.genome : Anolis_carolinensis\n-\n-# Aquilegia coerulea\n-aquiCoer.genome : Aquilegia_coerulea\n-\n-# Arabidopsis Thaliana\n-athaliana130.genome : Arabidopsis_Thaliana\n-athaliana130.reference : http://www.phytozome.net/dataUsagePolicy.php?org=Org_Athaliana\n-\n-athalianaTair9.genome : Arabidopsis_Thaliana\n-athalianaTair9.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release\n-\n-athalianaTair10.genome : Arabidopsis_Thaliana\n-athalianaTair10.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release\n-\n-# Bos taurus genes (Btau_4.0) (ENSEMBL)\n-btau4.0.59.genome : Bos_taurus\n-btau4.0.60.genome : Bos_taurus\n-btau4.0.61.genome : Bos_taurus\n-\n-# Otolemur garnettii genes (otoGar1) (ENSEMBL)\n-bushBaby1.60.genome : Otolemur_garnettii\n-bushBaby1.61.genome : Otolemur_garnettii\n-\n-# Candida_albicans_SC5314 \n-cAlbicansv21.genome: Candida_albicans_SC5314\n-cAlbicansv21.reference: http://www.candidagenome.org/download/gff/C_albicans_SC5314/\n-\n-# C. Briggsae \n-c_briggsae_WS230.genome : Caenorhabditis_briggsae\n-c_briggsae_WS230.reference : ftp://ftp.wormbase.org/pub/wormbase/releases/WS230/species/c_briggsae/\n-\n-# Cryptococcus neoformans\n-c_neoformans.genome: Cryptococcus_neoformans\n-c_neoformans.reference: http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiDownloads.html\n-\n-# Callithrix jacchus genes (calJac3) (ENSEMBL)\n-calJac3.2.1.60.genome : Callithrix_jacchus\n-calJac3.2.1.61.genome : Callithrix_jacchus\n-\n-# Canis familiaris genes (CanFam_2.0) (ENSEMBL)\n-canFam2.59.genome : Canis_familiaris\n-canFam2.60.genome : Canis_familiaris\n-canFam2.61.genome : Canis_familiaris\n-\n-# Felis catus genes (CAT) (ENSEMBL)\n-cat1.60.genome : Felis_catus\n-cat1.61.genome : Felis_catus\n-\n-# Cavia porcellus genes (cavPor3) (ENSEMBL)\n-cavPor3.60.genome : Cavia_porcellus\n-cavPor3.61.genome : Cavia_porcellus\n-\n-# Caenorhabditis elegans genes (WS210) (ENSEMBL)\n-ce.WS201.genome : Caenorhabditis_elegans\n-ce.WS210.60.genome : Caenorha"..b', GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Alternative_Yeast_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Ascidian_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Alternative_Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Blepharisma_Macronuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Chlorophycean_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Trematode_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Scenedesmus_obliquus_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-codon.Thraustochytrium_Mitochondrial: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n-\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml Fri Apr 20 11:22:59 2012 -0400 |
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| b'@@ -0,0 +1,482 @@\n+<tool id="snpEff" name="SnpEff" version="1.0">\n+\t<description>Variant efefct and annotation</description>\n+\t<!-- \n+\t You will need to change the path to wherever your installation is.\n+\t\tYou can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)\n+\t<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>\n+\t-->\n+\t<command>java -Xmx6G -jar /Users/pablocingolani/snpEff/snpEff.jar eff -c /Users/pablocingolani/snpEff/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>\n+\t<inputs>\n+\t\t<param format="Tabular" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>\n+\n+\t\t<param name="inputFormat" type="select" label="Input format">\n+\t\t\t<option value="vcf">VCF</option>\n+\t\t\t<option value="txt">Tabular</option>\n+\t\t\t<option value="pileup">Pileup</option>\n+\t\t\t<option value="bed">BED</option>\n+\t\t</param>\n+\n+\t\t<param name="outputFormat" type="select" label="Output format">\n+\t\t\t<option value="txt">Tabular</option>\n+\t\t\t<option value="vcf">VCF (only if input is VCF)</option>\n+\t\t\t<option value="bed">BED</option>\n+\t\t\t<option value="bedAnn">BED Annotations</option>\n+\t\t</param>\n+\n+\t\t<param name="genomeVersion" type="select" label="Genome">\n+\t\t\t\t<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>\n+\t\t\t\t<option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option>\n+\t\t\t\t<option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option>\n+\t\t\t\t<option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option>\n+\t\t\t\t<option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option>\n+\t\t\t\t<option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option>\n+\t\t\t\t<option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option>\n+\t\t\t\t<option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option>\n+\t\t\t\t<option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option>\n+\t\t\t\t<option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option>\n+\t\t\t\t<option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option>\n+\t\t\t\t<option value="agam2.6">Anopheles gambiae : agam2.6</option>\n+\t\t\t\t<option value="agam">Anopheles gambiae : agam</option>\n+\t\t\t\t<option value="aquiCoer">Aquilegia coerulea : aquiCoer</option>\n+\t\t\t\t<option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option>\n+\t\t\t\t<option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option>\n+\t\t\t\t<option value="athaliana130">Arabidopsis Thaliana : athaliana130</option>\n+\t\t\t\t<option value="alyrata107">Arabidopsis lyrata : alyrata107</option>\n+\t\t\t\t<option value="alyrata1">Arabidopsis lyrata : alyrata1</option>\n+\t\t\t\t<option value="amel2">Bee : amel2</option>\n+\t\t\t\t<option value="btau4.0.61">Bos taurus : btau4.0.61</option>\n+\t\t\t\t<option value="btau4.0.60">Bos taurus : btau4.0.60</option>\n+\t\t\t\t<option value="btau4.0.59">Bos taurus : btau4.0.59</option>\n+\t\t\t\t<option value="UMD3_1">Bos taurus : UMD3_1</option>\n+\t\t\t\t<option value="UMD3.1.66">Bos taurus : UMD3.1.66</option>\n+\t\t\t\t<option value="UMD3.1.65">Bos taurus : UMD3.1.65</option>\n+\t\t\t\t<option value="UMD3.1.64">Bos taurus : UMD3.1.64</option>\n+\t\t\t\t<option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option>\n+\t\t\t\t<option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option>\n+\t\t\t\t<option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option>\n+\t\t\t\t<option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option>\n+\t\t\t\t<option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option>\n+\t\t\t\t<option value="WS220.66">Caenorhabditis elegans : WS220.66</option>\n+\t\t\t\t<option value="WS220.65">Caenorhabditis elegans : WS220.'..b' belangeri : TREESHREW.63</option>\n+\t\t\t\t<option value="turTru1.66">Tursiops truncatus : turTru1.66</option>\n+\t\t\t\t<option value="turTru1.65">Tursiops truncatus : turTru1.65</option>\n+\t\t\t\t<option value="turTru1.64">Tursiops truncatus : turTru1.64</option>\n+\t\t\t\t<option value="turTru1.63">Tursiops truncatus : turTru1.63</option>\n+\t\t\t\t<option value="turTru1.61">Tursiops truncatus : turTru1.61</option>\n+\t\t\t\t<option value="turTru1.60">Tursiops truncatus : turTru1.60</option>\n+\t\t\t\t<option value="vacwr">Vaccinia Western Reserve : vacwr</option>\n+\t\t\t\t<option value="vibrio">Vibrio Cholerae : vibrio</option>\n+\t\t\t\t<option value="vicPac1.66">Vicugna pacos : vicPac1.66</option>\n+\t\t\t\t<option value="vicPac1.65">Vicugna pacos : vicPac1.65</option>\n+\t\t\t\t<option value="vicPac1.64">Vicugna pacos : vicPac1.64</option>\n+\t\t\t\t<option value="vicPac1.63">Vicugna pacos : vicPac1.63</option>\n+\t\t\t\t<option value="vicPac1.61">Vicugna pacos : vicPac1.61</option>\n+\t\t\t\t<option value="vicPac1.60">Vicugna pacos : vicPac1.60</option>\n+\t\t\t\t<option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option>\n+\t\t\t\t<option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option>\n+\t\t\t\t<option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option>\n+\t\t\t\t<option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option>\n+\t\t\t\t<option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option>\n+\t\t\t\t<option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option>\n+\t\t</param>\n+\n+\t\t<param name="udLength" type="select" label="Upstream / Downstream length">\n+\t\t\t<option value="0">No upstream / downstream intervals (0 bases)</option>\n+\t\t\t<option value="200">200 bases</option>\n+\t\t\t<option value="500">500 bases</option>\n+\t\t\t<option value="1000">1000 bases</option>\n+\t\t\t<option value="2000">2000 bases</option>\n+\t\t\t<option value="5000" selected="true">5000 bases</option>\n+\t\t\t<option value="10000">10000 bases</option>\n+\t\t\t<option value="20000">20000 bases</option>\n+\t\t</param>\n+\n+ <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">\n+\t\t\t<option value="">No filter (analyze everything)</option>\n+\t\t\t<option value="-hom">Analyze homozygous sequence changes only </option>\n+\t\t\t<option value="-het">Analyze heterozygous sequence changes only </option>\n+ </param>\n+\n+ <param name="filterIn" type="select" display="radio" label="Filter sequence changes">\n+\t\t\t<option value="">No filter (analyze everything)</option>\n+\t\t\t<option value="-del">Analyze deletions only </option>\n+\t\t\t<option value="-ins">Analyze insertions only </option>\n+\t\t\t<option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>\n+\t\t\t<option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>\n+ </param>\n+\n+ <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">\n+\t\t\t<option value="None" selected="true">None</option>\n+\t\t\t<option value="downstream">Do not show DOWNSTREAM changes </option>\n+\t\t\t<option value="intergenic">Do not show INTERGENIC changes </option>\n+\t\t\t<option value="intron">Do not show INTRON changes </option>\n+\t\t\t<option value="upstream">Do not show UPSTREAM changes </option>\n+\t\t\t<option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>\n+ </param>\n+\n+ <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">\n+\t\t\t<option value="">Use default (based on input type)</option>\n+\t\t\t<option value="-0">Force zero-based positions (both input and output)</option>\n+\t\t\t<option value="-1">Force one-based positions (both input and output)</option>\n+\t\t</param>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="tabular" name="output" />\n+\t\t<data format="html" name="statsFile" />\n+\t</outputs>\n+\n+\t<help>\n+\n+This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.\n+\n+For details about this tool, please go to http://snpEff.sourceforge.net\n+\n+\t</help>\n+</tool>\n+\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpEff_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff_download.xml Fri Apr 20 11:22:59 2012 -0400 |
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| b'@@ -0,0 +1,421 @@\n+<tool id="snpEff_download" name="SnpEff Download" version="1.0">\n+\t<description>Download a new database</description>\n+\t<command>java -jar /Users/pablocingolani/snpEff/snpEff.jar download -c /Users/pablocingolani/snpEff/snpEff.config $genomeVersion > $logfile </command>\n+\t<inputs>\n+\t\t<param name="genomeVersion" type="select" label="Genome">\n+\t\t\t\t<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>\n+\t\t\t\t<option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option>\n+\t\t\t\t<option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option>\n+\t\t\t\t<option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option>\n+\t\t\t\t<option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option>\n+\t\t\t\t<option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option>\n+\t\t\t\t<option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option>\n+\t\t\t\t<option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option>\n+\t\t\t\t<option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option>\n+\t\t\t\t<option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option>\n+\t\t\t\t<option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option>\n+\t\t\t\t<option value="agam2.6">Anopheles gambiae : agam2.6</option>\n+\t\t\t\t<option value="agam">Anopheles gambiae : agam</option>\n+\t\t\t\t<option value="aquiCoer">Aquilegia coerulea : aquiCoer</option>\n+\t\t\t\t<option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option>\n+\t\t\t\t<option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option>\n+\t\t\t\t<option value="athaliana130">Arabidopsis Thaliana : athaliana130</option>\n+\t\t\t\t<option value="alyrata107">Arabidopsis lyrata : alyrata107</option>\n+\t\t\t\t<option value="alyrata1">Arabidopsis lyrata : alyrata1</option>\n+\t\t\t\t<option value="amel2">Bee : amel2</option>\n+\t\t\t\t<option value="btau4.0.61">Bos taurus : btau4.0.61</option>\n+\t\t\t\t<option value="btau4.0.60">Bos taurus : btau4.0.60</option>\n+\t\t\t\t<option value="btau4.0.59">Bos taurus : btau4.0.59</option>\n+\t\t\t\t<option value="UMD3_1">Bos taurus : UMD3_1</option>\n+\t\t\t\t<option value="UMD3.1.66">Bos taurus : UMD3.1.66</option>\n+\t\t\t\t<option value="UMD3.1.65">Bos taurus : UMD3.1.65</option>\n+\t\t\t\t<option value="UMD3.1.64">Bos taurus : UMD3.1.64</option>\n+\t\t\t\t<option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option>\n+\t\t\t\t<option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option>\n+\t\t\t\t<option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option>\n+\t\t\t\t<option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option>\n+\t\t\t\t<option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option>\n+\t\t\t\t<option value="WS220.66">Caenorhabditis elegans : WS220.66</option>\n+\t\t\t\t<option value="WS220.65">Caenorhabditis elegans : WS220.65</option>\n+\t\t\t\t<option value="WS220.64">Caenorhabditis elegans : WS220.64</option>\n+\t\t\t\t<option value="WS220.63">Caenorhabditis elegans : WS220.63</option>\n+\t\t\t\t<option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option>\n+\t\t\t\t<option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option>\n+\t\t\t\t<option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option>\n+\t\t\t\t<option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option>\n+\t\t\t\t<option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option>\n+\t\t\t\t<option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option>\n+\t\t\t\t<option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option>\n+\t\t\t\t<option value="canFam2.61">Canis familiaris : canFam2.61</option>\n+\t\t\t\t<option value="canFam2.60">Canis familiaris : canFam2.60</option>\n+\t\t\t\t<option value="canFam2.59">Canis familiaris : canFam2.59</option>\n+\t\t\t\t<option value="BROADD2.66">Canis familiaris : BROADD2.66</option>\n+\t\t\t\t<option value="BROADD2.65">Canis familiaris : BROADD2.65</option>\n+\t\t\t\t<option value="BROADD2.64">Canis familiaris : BROADD2.64</option>\n+\t\t\t\t<option '..b'pes : fugu4.60</option>\n+\t\t\t\t<option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option>\n+\t\t\t\t<option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option>\n+\t\t\t\t<option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option>\n+\t\t\t\t<option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option>\n+\t\t\t\t<option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option>\n+\t\t\t\t<option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option>\n+\t\t\t\t<option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option>\n+\t\t\t\t<option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option>\n+\t\t\t\t<option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option>\n+\t\t\t\t<option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option>\n+\t\t\t\t<option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option>\n+\t\t\t\t<option value="testHg3765Chr22">TestCase : testHg3765Chr22</option>\n+\t\t\t\t<option value="testHg3763ChrY">TestCase : testHg3763ChrY</option>\n+\t\t\t\t<option value="testHg3763Chr20">TestCase : testHg3763Chr20</option>\n+\t\t\t\t<option value="testHg3763Chr1">TestCase : testHg3763Chr1</option>\n+\t\t\t\t<option value="testHg3761Chr16">TestCase : testHg3761Chr16</option>\n+\t\t\t\t<option value="testHg3761Chr15">TestCase : testHg3761Chr15</option>\n+\t\t\t\t<option value="testCase">TestCase : testCase</option>\n+\t\t\t\t<option value="test">TestCase : test</option>\n+\t\t\t\t<option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option>\n+\t\t\t\t<option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option>\n+\t\t\t\t<option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option>\n+\t\t\t\t<option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option>\n+\t\t\t\t<option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option>\n+\t\t\t\t<option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option>\n+\t\t\t\t<option value="SL2.40">Tomato : SL2.40</option>\n+\t\t\t\t<option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option>\n+\t\t\t\t<option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option>\n+\t\t\t\t<option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option>\n+\t\t\t\t<option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option>\n+\t\t\t\t<option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option>\n+\t\t\t\t<option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option>\n+\t\t\t\t<option value="turTru1.66">Tursiops truncatus : turTru1.66</option>\n+\t\t\t\t<option value="turTru1.65">Tursiops truncatus : turTru1.65</option>\n+\t\t\t\t<option value="turTru1.64">Tursiops truncatus : turTru1.64</option>\n+\t\t\t\t<option value="turTru1.63">Tursiops truncatus : turTru1.63</option>\n+\t\t\t\t<option value="turTru1.61">Tursiops truncatus : turTru1.61</option>\n+\t\t\t\t<option value="turTru1.60">Tursiops truncatus : turTru1.60</option>\n+\t\t\t\t<option value="vacwr">Vaccinia Western Reserve : vacwr</option>\n+\t\t\t\t<option value="vibrio">Vibrio Cholerae : vibrio</option>\n+\t\t\t\t<option value="vicPac1.66">Vicugna pacos : vicPac1.66</option>\n+\t\t\t\t<option value="vicPac1.65">Vicugna pacos : vicPac1.65</option>\n+\t\t\t\t<option value="vicPac1.64">Vicugna pacos : vicPac1.64</option>\n+\t\t\t\t<option value="vicPac1.63">Vicugna pacos : vicPac1.63</option>\n+\t\t\t\t<option value="vicPac1.61">Vicugna pacos : vicPac1.61</option>\n+\t\t\t\t<option value="vicPac1.60">Vicugna pacos : vicPac1.60</option>\n+\t\t\t\t<option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option>\n+\t\t\t\t<option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option>\n+\t\t\t\t<option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option>\n+\t\t\t\t<option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option>\n+\t\t\t\t<option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option>\n+\t\t\t\t<option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option>\n+\t\t</param>\n+\t</inputs>\n+\n+\t<outputs>\n+\t\t<data format="txt" name="logfile" />\n+\t</outputs>\n+\n+\t<help>\n+\n+This tool downloads a SnpEff database.\n+\n+For details about this tool, please go to http://snpEff.sourceforge.net\n+\n+\t</help>\n+</tool>\n+\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_annotate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_annotate.xml Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,24 @@ +<tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0"> + <description>Annotate SNPs from dbSnp</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command>java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar annotate -q $dbSnp $input > $output </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param format="Tabular" name="dbSnp" type="data" label="dbSnp in VCF format"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +This is typically used to annotate IDs from dbSnp. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate + + </help> +</tool> + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_caseControl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_caseControl.xml Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,35 @@ +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0"> + <description>Count samples are in 'case' and 'control' groups.</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command> + java -Xmx1G -jar /home/pcingola/tools/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param name="hhCase" type="select" label="Hom/Het case"> + <option value="any">Any</option> + <option value="hom">Homozygous</option> + <option value="het">Heterozygous</option> + </param> + <param name="hhControl" type="select" label="Hom/Het control"> + <option value="any">Any</option> + <option value="hom">Homozygous</option> + <option value="het">Heterozygous</option> + </param> + <param name="caseControStr" type="text" label="Case / Control" size="50"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol + + </help> +</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,33 @@ +<tool id="snpSift_filter" name="SnpSift Filter" version="1.0"> + <options sanitize="False" /> + <description>Filter variants using arbitrary expressions</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output + --> + <command> + java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param name="expr" type="text" label="Expression" size="50"/> + </inputs> + <configfiles> + <configfile name="exprFile"> + $expr + </configfile> + </configfiles> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +You can filter using arbitrary expressions. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter + + </help> +</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_int.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_int.xml Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,25 @@ +<tool id="snpSift_int" name="SnpSift Intervals" version="1.0"> + <description>Filter variants using intervals </description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command> + cat $input | java -Xmx2G -jar /home/pcingola/tools/SnpSift.jar int $bedFile > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param format="Tabular" name="bedFile" type="data" label="Intervals (BED file)"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +You can filter using intervals (BED file) + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals + + </help> +</tool> |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/galaxy/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/galaxy/tool_conf.xml Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,13 @@ + + <!-- + Add this section to tool_conf.xml file in your Galaxy distribution + --> + <section name="SnpEff tools" id="snpEff_tools"> + <tool file="snpEff/snpEff.xml" /> + <tool file="snpEff/snpEff_download.xml" /> + <tool file="snpEff/snpSift_annotate.xml" /> + <tool file="snpEff/snpSift_caseControl.xml" /> + <tool file="snpEff/snpSift_filter.xml" /> + <tool file="snpEff/snpSift_int.xml" /> + </section> + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/bam2fastq.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/bam2fastq.pl Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,8 @@ +#!/usr/bin/perl + +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/, $l; + print "\@$t[0]\n$t[9]\n+\n$t[10]\n"; +} + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/buildTestCases.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/buildTestCases.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,16 @@ +#!/bin/sh + +# Test cases hg37 +./scripts/snpEffM.sh build -v -txt testCase + +# Test cases hg37.61 +./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr15 +./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr16 + +# Test cases hg37.63 +./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr1 +./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr20 +./scripts/snpEffM.sh build -v -gtf22 testHg3763ChrY + +# Test cases hg37.65 +./scripts/snpEffM.sh build -v -gtf22 testHg3765Chr22 |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/build_regulation.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/build_regulation.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,5 @@ +#!/bin/sh + +./scripts/queue.pl 10 24 15 queue_build_regulation.txt + + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/compareToEnsembl.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/compareToEnsembl.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,8 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ + +java -Xmx3G \ + -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ + ca.mcgill.mcb.pcingola.testCases.CompareToEnsembl \ + $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/GRCh37.64/._countBioTypes.pl |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,71 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Count unmber of bioType for transcript (second column in GTF file) and +# for gene ('/gene_biotype' info field) +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +use strict; + +my($count, %count, $countMatch) = (0, 0); + +#--- +# Process input (GTF file) +#--- +my($l, $key, $field, @t, %bioType); +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/, $l; + + # Get transcript biotype + my($bioTypeTr) = $t[1]; + die "Cannot find biotype" if( $bioTypeTr eq '' ); + + # Get gene biotype + @t = split /;/, $t[8]; + my($bioTypeGene) = ''; + foreach $field ( @t ) { + # Parse 'name value' fields + if( $field =~/\s*(.*)\s\"(.*)\"/ ) { + my($name, $value) = ($1, $2); + if( $name eq 'gene_biotype' ) { $bioTypeGene = $value; } + } + } + die "Cannot find biotype" if($bioTypeGene eq ''); + + $bioType{$bioTypeTr} = 1; + $bioType{$bioTypeGene} = 1; + + $key = "$bioTypeTr\t$bioTypeGene"; + $count{$key}++; + + # Count + if( $bioTypeTr eq $bioTypeGene ) { $countMatch++; } + $count++; +} + +#--- +# Show results +#--- +foreach $key ( sort keys %count ) { print "$count{$key}\t$key\n"; } +print "Count\t$count\n"; +print "Count match\t$countMatch\n"; + +#--- +# Show as table +#--- +my($bt, $bg); +print "\t"; +foreach $bg ( sort keys %bioType ) { print "$bg\t"; } +print "\n"; +foreach $bt ( sort keys %bioType ) { + print "$bt\t"; + foreach $bg ( sort keys %bioType ) { + $key = "$bt\t$bg"; + print "$count{$key}\t"; + } + print "\n"; +} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/create.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/create.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,26 @@ +#!/bin/sh + +# wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz + +# GFF has to be downloaded manually from +# +# http://solgenomics.net/itag/release/2.3/list_files# +# File ITAG2.3_gene_models.gff3 +# +# + +# Create genes.gff +echo Decompressing the file +cp ITAG2.3_gene_models.gff3.gz genes.gff.gz +rm -f genes.gff +gunzip genes.gff.gz + +echo Fixing start-end problem +cat genes.gff | ./fixStartEnd.pl > g +mv g genes.gff + +# Append FASTA Sequences +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/fixStartEnd.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/fixStartEnd.pl Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,19 @@ +#!/usr/bin/perl + +# +# If start > end swap values +# +while( $l = <STDIN> ) { + chomp $l; + @t = (); + @t = split /\t/, $l; + + ($start, $end) = ($t[3], $t[4]); + if( $start > $end ) { + #print STDERR "ERROR:\t$l\n"; + ($t[3], $t[4]) = ($t[4], $t[3]); + $l = join "\t", @t; + } + + print "$l\n"; +} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,56 @@ +#!/usr/bin/perl + + +# Parse command line argument +$gtfFile = $ARGV[0]; + +#--- +# Pass one: Get geneID -> transcriptID +# Note: It is assumed (and it is true for this particular file) that each genes has only one transcript +# This assumption os obviously not true for other files & other organisms +#---- +print STDERR "Pass 1: Read IDs\n"; +open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; + +while( $l = <GTF> ) { + chomp $l; + ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; + + $gid = $tid = ""; + if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } + if( $attr =~ /transcript_id "(.*?)";/ ) { $tid = $1; } + + if(( $gid ne '' ) && ( $tid ne '' )) { + # print "\tgid = $gid\n\ttid = $tid\n"; + + # Store transcriptId + if( $tbyg{$gid} eq '' ) { $tbyg{$gid} = $tid; } + + # Is there more than one transcript per gene? => Error + if( $tbyg{$gid} ne $tid ) { die "Error: More than one transcript per gene. We cannot map transcripts!\n\t$tid ne $tbyg{$gid}\n"; } + } +} + +close GTF; + +#--- +# Pass two: Fill in the missing transcript IDs +#--- +print STDERR "Pass 2: Add ID data\n"; +open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; + +while( $l = <GTF> ) { + chomp $l; + ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; + + $gid = ""; + if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } + elsif( $attr =~ /gene_id "(.*)"/ ) { $gid = $1; } + else { print STDERR "Cannot match '$attr'\n"; } + $tid = $tbyg{$gid}; + + if(( $gid ne '' ) && ( $tid ne '' )) { print "$seqname\t$source\t$feature\t$start\t$end\t$score\t$strand\t$frame\tgene_id \"$gid\"; transcript_id \"$tid\";\n"; } + else { print STDERR "Skipping line: $l\n\tgid = '$gid'\n\ttid = '$tid'\n"; } +} + +close GTF; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/alyrata1/convert.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,11 @@ +#!/bin/sh + +zcat Araly1_GeneModels_FilteredModels6.gff.gz \ + | sed "s/name/gene_id/" \ + | sed "s/transcriptId \(.*\)/transcript_id \"\1\";/" \ + | sed "s/exonNumber \(.*\)/exon_number \"\1\";/" \ + > g1 + +./convert.pl g1 > genes.gtf +rm -vf g1 + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/c_briggsae_WS230/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,15 @@ +#!/bin/sh -e + +zcat c_briggsae.WS230.annotations.gff3.gz \ + | grep -v SNP \ + | grep -v translated_nucleotide_match \ + | grep -v repeat_region \ + | grep -v inverted_repeat \ + | grep -v tandem_repeat \ + | grep -v nucleotide_match \ + > genes.gff + +# Add fasta sequence +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +zcat c_briggsae.WS230.genomic.fa.gz >> genes.gff |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/genomes/x.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/genomes/x.sh Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,8 @@ +#!/bin/sh + +for chr in chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr1.fa chr20.fa chr21.fa chr22.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chrMT.fa chrX.fa chrY.fa +do + MDGR=`cat GRCh37.65/$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` + MDHG=`cat hg19/chr$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` + echo -e "$chr\n\t$MDGR\n\t$MDHG" +done |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/._create.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,35 @@ +#!/bin/sh -e + +echo "Processing GFF file" +gunzip -c Gmax_109_gene.gff3.gz > genes.gff +# | sed "s/.five_prime_UTR.1//" \ +# | sed "s/.three_prime_UTR.1//" \ +# > genes.gff + +echo "Adding FASTA sequence" +( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff + +ehco "Create CDS file" +gunzip -c Gmax_109_cds.fa.gz \ + | sed "s/|PACid:/|PAC:/" \ + | sed "s/Glyma.*|//" \ + > cds.fa + +echo "Create protein file" +gunzip -c Gmax_109_peptide.fa.gz \ + | sed "s/|PACid:/|PAC:/" \ + | sed "s/Glyma.*|//" \ + > protein.fa + +# Build databse +cd $HOME/snpEff + +./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build + +# CDS test +./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds + +cd - + +echo Done! + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/hg19/create.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/hg19/create.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,52 @@ +#!/bin/sh + +REF=hg19 + +#--- +# Download latest datasets +#--- + +# # Genome sequence +# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/bigZips/chromFa.tar.gz +# +# # Protein sequences +# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz +# +# # CDS sequences +# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz +# +# # RefLink +# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/database/refLink.txt.gz +# +# #--- +# # Create files +# #--- +# gunzip refLink.txt.gz +# +# # Protein fasta +# zcat human.protein.faa.gz | ../../scripts/proteinFasta2NM.pl refLink.txt > protein.fa +# gzip protein.fa +# +# # CDS fasta +# zcat human.rna.fna.gz | sed "s/^>gi|[0-9]*|ref|\(.*\)\..*|.*/>\1/" > cds.fa +# gzip cds.fa + +# Chromosome fasta +#rm -rvf chr +#mkdir chr +cd chr +#tar -xvzf ../chromFa.tar.gz + +FASTA=../$REF.fa +echo Creating FASTA file +rm -vf $FASTA +cat chr[1-9].fa >> $FASTA +cat chr??.fa >> $FASTA +cat chr[A-Z].fa >> $FASTA +cat chr???*.fa >> $FASTA + +cd - + +# # Compress genome file +# $HOME/tools/pigz/pigz hg19.fa +# cp hg19.fa.gz $HOME/snpEff/data/genomes/ |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA01/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA01/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_002516.2.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_002516.2.fna >> genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA14/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA14/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/paeru.PA14/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_008463.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_008463.1.fna >> genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/._genes.sh |
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| Binary file snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/._genes.sh has changed |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_009444.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_009444.1.fna >> genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/._genes.sh |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_012660.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_012660.1.fna >> genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/._genes.sh |
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| Binary file snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/._genes.sh has changed |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/ppersica139/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,8 @@ +#!/bin/sh + +# Download files +#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139.fa.gz +#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139_gene.gff3.gz + +( zcat Ppersica_139_gene.gff3.gz ; echo "###" ; echo "##FASTA" ; zcat Ppersica_139.fa.gz ) > genes.gff + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._genes.sh |
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| Binary file snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._genes.sh has changed |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._mRnaAddParent.pl |
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| Binary file snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/._mRnaAddParent.pl has changed |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/genes.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/genes.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,7 @@ +#!/bin/sh + +cat ORI/build5_locus.gff3 > genes.gff +cat ORI/build5_genes.gff3 | ./mRnaAddParent.pl >> genes.gff +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +cat ORI/IRGSPb5.fa >> genes.gff |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,28 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# Add 'Parent' option in mRNA lines +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/,$l; + + $type = $t[2]; + + # Is it an mRNA? + if( $type eq 'mRNA' ) { + # Parse ID in options + $opts = $t[8]; + if( $opts =~ /ID=(.*?)-\d+;/ ) { + $pid = $1; + $pid =~ tr/t/g/; + # Add 'Parent' option + $l .= ";Parent=$pid"; + } + } + + print "$l\n"; +} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/distro.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/distro.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,47 @@ +#!/bin/sh + +#------------------------------------------------------------------------------ +# Create a zip file for distribution +# Note: Only binary data is included (no raw gene info / genomes) +# +# Pablo Cingolani 2010 +#------------------------------------------------------------------------------ + +VERSION="2_1" +VERSION_REV=$VERSION"a" +DIR=$HOME/snpEff_$VERSION_REV +rm -rvf $DIR +mkdir $DIR + +# Copy core files +cp snpEff.config snpEff.jar $DIR +cp -rvfH galaxy scripts $DIR + +cd $DIR +rm -rvf `find . -name "CVS" -type d` +cd - + +# Create 'core' zip file +cd $HOME +ZIP="snpEff_v"$VERSION_REV"_core.zip" +rm -f $ZIP 2> /dev/null +zip -r $ZIP snpEff_$VERSION_REV +cd - + +# Create ZIP file for each database +for d in `ls data/*/snpEffectPredictor.bin` +do + DIR=`dirname $d` + GEN=`basename $DIR` + + echo $GEN + ZIP="snpEff_v"$VERSION"_"$GEN".zip" + zip -r $ZIP data/$GEN/*.bin +done + +# Look for missing genomes +echo Missing genomes: +ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt +ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt +diff genomes_dirs.txt genomes_bins.txt | grep "^<" + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/download.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/download.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,120 @@ +#!/bin/sh -e + +RELEASE=66 + +# mkdir download +cd download + +#--- +# Download +#--- + +# # Download GTF files (annotations) +# wget -r -A "*gtf.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" +# +# # Download FASTA files (reference genomes) +# wget -r -A "*toplevel.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" +# +# # Download CDS sequences +# wget -r -A "*cdna.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" +# +# # Download PROTEIN sequences +# wget -r -A "*.pep.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" + +#--- +# Create directory structure +#--- + +# # Move all downloaded file to this directory +# mv `find ftp.ensembl.org -type f` . + +# # Gene annotations files +# for gtf in *.gtf.gz +# do +# short=`../scripts/file2GenomeName.pl $gtf | cut -f 5` +# echo ANNOTATIONS: $short +# +# mkdir -p data/$short +# cp $gtf data/$short/genes.gtf.gz +# done +# +# # Reference genomes files +# mkdir -p data/genomes +# for fasta in *.dna.toplevel.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# echo REFERENCE: $genome +# +# cp $fasta data/genomes/$genome.fa.gz +# done +# +# # CDS genomes files +# for fasta in *.cdna.all.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# echo CDS: $genome +# +# cp $fasta data/$genome/cds.fa.gz +# done +# +# # Protein seuqence files +# for pep in *.pep.all.fa.gz +# do +# short=`../scripts/file2GenomeName.pl $pep | cut -f 5` +# echo PROTEIN: $short +# +# mkdir -p data/$short +# cp $pep data/$short/protein.fa.gz +# done + +#--- +# Config file entries +#--- + +# for fasta in *.cdna.all.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 4` +# short=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# +# # Individual genome entry +# echo -e "$short.genome : $genome" +# echo -e "$short.reference : ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" +# echo +# done + +# Back to parent dir +cd - > /dev/null + +#--- +# Create build queue entries +#--- + +# rm -vf queue_build.txt +# +# # Build from TXT files +# for genes in data/*/genes.txt* +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v $genomeName" +# done | sort >> queue_build.txt +# +# # Build from GFF2 files +# echo "./scripts/snpEffXL.sh build -v -gff2 amel2" >> queue_build.txt +# +# # Build from GFF3 files +# for genes in `ls data/*/genes.gff* | grep -v amel2` +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v -gff3 $genomeName" +# done | sort >> queue_build.txt +# +# # Build from GTF22 files +# for genes in data/*/genes.gtf* +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v -gtf22 $genomeName" +# done | sort >> queue_build.txt + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/fasta2tab.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/fasta2tab.pl Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,32 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# Split a fasta file (create one file per sequence) +# +# +#------------------------------------------------------------------------------ + +use strict; + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ + +my($seq, $name) = ('', ''); +my($lineNum, $l, $newName); +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + chomp $l; + if( $l =~/^>\s*(.*)\s*$/ ) { + $newName = $1; + if( $seq ne "" ) { print "$name\t$seq\n"; } + # New sequence + $name = $newName; + $seq = ""; + } else { $seq .= $l; } +} + +if( $seq ne "" ) { print "$name\t$seq\n"; } + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/fastaSample.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/fastaSample.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,41 @@ +#!/usr/bin/perl + +#--- +# Initialize parameters +#--- +$sampleStart = $ARGV[0]; +$sampleEnd = $ARGV[1]; +if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; } + +$sampleStart--; +$sampleEnd--; +$sampleLen = $sampleEnd - $sampleStart + 1; + +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + if( $l =~/^>/ ) { + # Sample if not empty + if( $seq ne "" ) { + $s = substr( $seq, $sampleStart, $sampleLen); + print "$s\n"; + } + # New sequence + $seq = ""; + } else { + chomp($l); + $seq .= $l; + } +} + +# Sample if not empty +if( $seq ne "" ) { + $s = substr( $seq, $sampleStart, $sampleLen); + print "$s\n"; +} + +$len = length($seq); +print STDERR "Lines: $lineNum\n"; +print STDERR "Sequence size: $len\n"; +print STDERR "Sample size: $sampleLen\n"; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/fastaSplit.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/fastaSplit.pl Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,42 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# Split a fasta file (create one file per sequence) +# +# +#------------------------------------------------------------------------------ + +use strict; + +#------------------------------------------------------------------------------ +# Write fasta file +#------------------------------------------------------------------------------ +sub writeSeq($$) { + my($name, $seq) = @_; + $name = "chr" . $name . ".fa"; + print "Writing to $name\n"; + open OUT, "> $name"; + print OUT $seq; + close OUT; +} + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ + +my($seq, $name) = ('', ''); +my($lineNum, $l, $newName); +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + if( $l =~/^>\s*(.*?)\s+.*/ ) { + $newName = $1; + if( $seq ne "" ) { writeSeq($name, $seq); } + # New sequence + $name = $newName; + $seq = $l; + } else { $seq .= $l; } +} + +if( $seq ne "" ) { writeSeq($name, $seq); } |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/file2GenomeName.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/file2GenomeName.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,24 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Transform file name to genome short name +# +#------------------------------------------------------------------------------- + +$file = $ARGV[0]; +print "$file"; + +$base = `basename $file`; +chomp $base; +print "\t$base"; + +if( $base =~ /(.*?)\.(.*)\..?dna\.(.*)\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } +elsif( $base =~ /(.*?)\.(.*)\.gtf\.gz/ ) { ($gen, $short) = ($1, $2); } +elsif( $base =~ /(.*?)\.(.*)\.pep\.all\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } +$full = "$gen.$short"; +print "\t$full\t$gen\t$short"; + + +print "\n"; + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictions.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictions.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +#!/bin/sh + +# Remove some (boring) predictions +grep -v DOWNSTREAM \ + | grep -v UPSTREAM \ + | grep -v INTRON \ + | grep -v UTR_5_PRIME \ + | grep -v UTR_3_PRIME \ + | grep -v INTERGENIC \ + | grep -v " SYNONYMOUS_CODING" \ + | grep -v WITHIN_NON_CODING_GENE |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,6 @@ +#!/bin/sh + +# Keep interesting predictions +java -jar $HOME/tools/VcfEtc.jar filter \ + "( EFF =~ 'NON_SYN' ) | ( EFF =~ 'CODON') | ( EFF =~ 'SPLICE') | ( EFF =~ 'STOP') | ( EFF =~ 'START') | ( EFF =~ 'FRAME') | ( EFF =~ 'LOST') | ( EFF =~ 'DELETED' )" \ + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/genesTxtColumnNames.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/genesTxtColumnNames.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,33 @@ +#!/bin/sh + +#------------------------------------------------------------------------------- +# Convert the gene names in order to be used in an R script +# +# Usage: cat snpEff_genes.txt | ./scripts/genesTxtColumnNames.sh > genes.txt +# +# Once in R, you can: +# - Load this table: +# data <- read.csv("genes.txt", sep= "\t", header=TRUE); +# +# - Access the data: +# data$countINTRON +# +# - Add missing or empty columns: +# if( is.null(data$countINTRON ) { data$countINTRON <- 0 * (1:length(data$geneId) ); } +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +cat \ + | grep -v "^# The following"\ + | sed "s/Bases affected (/bases/g" \ + | sed "s/Length (/len/g" \ + | sed "s/Count (/count/g" \ + | sed "s/Total score (/score/g" \ + | sed "s/)//g" \ + | sed "s/#GeneId/geneId/" \ + | sed "s/GeneName/geneName/" \ + | sed "s/BioType/bioType/" \ + | sed "s/_PRIME//g" \ + | sed "s/SPLICE_SITE_//g" \ + | sed "s/SYNONYMOUS_CODING/SYN/g" \ |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/hist.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/hist.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,88 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a histogram (using R) +# Data is feed as a 1 column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'hist'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R vector +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + + # Does the string contain exactly one number? (can be float) + if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } +} +close TXT; + +#--- +# Create an R program, save histogram plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +histDens <- function( x, title, q=1.0, breaks = 30 ) { + # Show only this part of the data + xmin <- quantile( x, 1-q ) + xmax <- quantile( x, q ) + data <- x[ (x >= xmin) & (x <= xmax) ]; + + dens <- density(data) + + h <- hist(data, main=title, xlab = "data", ylab = "Frequency", freq = T, breaks=breaks); + + # Adjust density height to 'frecuency' + dens\$y <- max(h\$counts) * dens\$y/max(dens\$y) + lines(dens, col='red') + + # Mean & median calculated over the whola data + abline( v=mean(x), col='blue', lty=2, lwd=2); + abline( v=median(x), col='green', lty=2, lwd=2); + + legend("topright",c("Mean","Median"),lty=c(1,1),col=c("blue","green")) + +} + +png('$pngFile', width = 1024, height = 1024); +par( mfrow=c(2,1) ); + +data <- read.csv("$txtFile", sep='\\t', header = TRUE); +x <- data\$x + +histDens( x, "Histogram: All data", 1.0 ); +histDens( x, "Histogram: Quantile [2% - 98%]", 0.98 ); + +print( summary( x ) ) + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/joinSnpEff.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/joinSnpEff.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,125 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# +# Mark snps as X1, X2 or 'Both' +# +#------------------------------------------------------------------------------ + +use strict; + +my($debug) = 0; + +#------------------------------------------------------------------------------ +# Read a file and index lines by SNP +#------------------------------------------------------------------------------ +sub readSnps($) { + my($file) = (@_); + my($l, %snps); + + open SNP, $file || die "Cannot open file '$file'\n"; + while( $l = <SNP> ) { + my($chr, $pos, $ref, $var) = split /\t/, $l; + my($snp) = "$chr:$pos\_$ref/$var"; + $snps{$snp} .= $l; + } + close SNP; + return %snps; +} + +#------------------------------------------------------------------------------ +# Print SNP info and quals +#------------------------------------------------------------------------------ +sub printLine($$$$) { + my($snp, $lines, $quals, $q) = (@_); + my($line, @lines); + (@lines) = split '\n', $lines; + foreach $line ( @lines ) { + my($l) = replaceSnpQ($line, $q); + print "$l\t$quals\n"; + } +} + +#------------------------------------------------------------------------------ +# Parse snp quality parameter +#------------------------------------------------------------------------------ +sub parseSnpQ($) { + my($l) = @_; + my(@t); + (@t) = split /\t/,$l; + return $t[6]; +} + +#------------------------------------------------------------------------------ +# Replace a quality +#------------------------------------------------------------------------------ +sub replaceSnpQ($$) { + my($line, $q) = @_; + my(@t); + (@t) = split /\t/, $line; + $t[1] = $q; + return join("\t", @t); +} + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ +# Read arguments +my(@file); +(@file) = @ARGV; +if( $#file <= 0 ) { die "Usage: ./joinSnpEff.pl tag1 file1 tag2 file2 ... tagN fileN\n"; } + +# Parse arguments +print STDERR "Reading files:\n"; +my($i, $j, $file, $tag, $snp, @snpsAll, %snps, @tags); +for( $i=0 , $j=0 ; $i < $#ARGV ; $i+=2, $j++ ) { + # Read tag + $tags[$j] = $tag = $ARGV[$i]; + + # Read file + $file = $ARGV[$i+1]; + if( $file eq '' ) { die "Missing file for tag '$tag'\n"; } + print STDERR "\tTags[$j]: $tag\t'$file'\n"; + %snps = readSnps($file); + + # Add all snps + foreach $snp ( keys %snps ) { $snpsAll[$j]->{$snp} = $snps{$snp}; } +} + +#--- +# Print SNPS +#--- +my($snp, %done, %snpsi); +my($j, $jj); +$i = 0; +print STDERR "Joining SNP from all files\n"; +for( $i=0 ; $i <= $#tags ; $i++ ) { # For all tags + print "TAG:\ttags[$i] = '$tags[$i]'\n" if $debug; + my($uniq, $shared) = (0, 0); + %snpsi = %{$snpsAll[$i]}; + foreach $snp (sort keys %snpsi) { # For all snps... + if( ! $done{$snp} ) { # Not done yet? + + # Get qualities from all SNPs + my($quals, $qSum, $qCount) = ("", 0, 0); + my($all) = "ALL "; + for( $j=0, $jj=1 ; $j <= $#snpsAll ; $j++ , $jj++ ) { + if( exists $snpsAll[$j]{$snp} ) { + my($q) = parseSnpQ($snpsAll[$j]->{$snp}); + $quals .= "$tags[$j]:$q "; + $qSum += $q; + $qCount++; + } else { $all = ""; } + } + + if( $qCount <= 1 ) { $uniq++; } # Count unique SNPs for this file + else { $shared++; } + + $done{$snp} = 1; + my($qAvg) = ( $qCount > 0 ? int($qSum/$qCount) : 0); + printLine($snp, $snpsi{$snp}, "$all $quals", $qAvg); + } else { $shared++; } + } + print STDERR "\tTags[$i]: $tags[$i]\tUnique / Shared snps: $uniq / $shared\n"; +} + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/nOutOfM.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/nOutOfM.pl Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,10 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Keep variants present in N out of M samples (multi-sample VCF file) +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/promoterSequences.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/promoterSequences.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,8 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ + +java -Xmx3G \ + -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ + ca.mcgill.mcb.pcingola.PromoterSequences \ + $* |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/proteinFasta2NM.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/proteinFasta2NM.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,45 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Convert fasta headers from protein ID (NP_XXXX) into transcript ID NM_XXXX +# +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +# Parse command line arguments +$refLink = $ARGV[0]; +die "Usage: cat file.fasta | ./proteinFasta2NM.pl refLink.txt > protein_NM.fasta" if $refLink eq ''; + +# Read refLink file +open RL, $refLink or die "Cannot opne file '$refLink'\n"; +while( <RL> ) { + chomp; + @t = split /\t/; + ($nm, $np) = ($t[2], $t[3]); + + if( $np ne '' ) { + if( $trId{$np} ne '' ) { print STDERR "Error: Non empty entry '$np' = $trId{$np}\n"; } + else { $trId{$np} = $nm; } + } +} + +# Read fasta file +while( <STDIN> ) { + chomp; + + if( /^>(.*)/ ) { # Header? => change form protein NP_XXX to transcript NM_XXXX + # Get NM_ field + @t = split /\|/; + $np = $t[3]; + + # Remove anything after the dot + if( $np =~ /(.*)\./ ) { $np = $1; } + + # Found a transcript ID? + if( $trId{$np} ne '' ) { print ">$trId{$np}\n"; } + else { print "$l\n"; } + } else { print "$_\n"; } # Show line +} + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/qqplot.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/qqplot.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,80 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a QQ plot (using R) +# Data is feed as a 1 column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'QQ-plot'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R vector +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + + # Does the string contain exactly one number? (can be float) + if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } +} +close TXT; + +#--- +# Create an R program, save QQ-plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +qqplot <- function( x, title ) { + keep <- (x > 0) & (x <= 1) & ( ! is.na(x) ); + x <- x[keep] + s <- sort(x); + ly <- -log10(s); + + n <- length(s); + lx <- -log10( (1:n) / (n+1) ) + + # Show auto range + #par( mfrow=c(2,1) ); + #plot( lx, ly, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); + #abline( 0 , 1 , col='red'); + + # Show full range in both plots + range <- c(0 , max(lx, ly) ); + plot( lx, ly, xlim=range, ylim=range, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); + abline( 0 , 1 , col='red'); +} + +png('$pngFile', width = 1024, height = 1024); + +data <- read.csv("$txtFile", sep='\t', header = TRUE); +qqplot( data\$x, "$base" ); + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; + |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue.pl Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,127 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# Simple queue management program +# Attempts to keep 'numProc' processes running at the same time +# +# Proceses are defined in a file (one line per process) +# +# Every executed process creates two files: 'pid.stdout' and 'pid.stderr' where +# pid is the process ID. The files contain STDOUT and STDERR for that process. +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +use strict; +use POSIX; + + +my($uptimeCmd) = "/usr/bin/uptime"; # Uptime command +my($maxUptime); +$| = 1; # Don't use buffers for STDIN/STDOUT + +#------------------------------------------------------------------------------- +# Should a new process be run? +# Check some conditions before trying to run the next process +#------------------------------------------------------------------------------- +sub shouldRun() { + if( $maxUptime < 0 ) { return 1; } # Always true if $maxUptime is negative + my($utRes) = `$uptimeCmd`; + my($ut) = 0; + if( $utRes =~ /load average:\s+(\d+\.\d+),/ ) { $ut = $1; } + return $ut < $maxUptime; +} + +#------------------------------------------------------------------------------- +# Print something 'printLog' style +#------------------------------------------------------------------------------- +sub printLog($) { + my($str) = @_; + my($now) = strftime "%Y-%m-%d %H:%M:%S", localtime; + print "$now\t$str\n"; +} + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- +# Usage: queue numProc File +my($maxNumProc, $sleepTime, $file); +($maxNumProc, $maxUptime, $sleepTime, $file) = @ARGV; +if( $file eq '' ) { + print "Usage: queue.pl maxNumProc maxUptime sleepTime file\n"; + print "Where:\n"; + print "\tnumProc Number of simultaneous processes\n"; + print "\tmaxUptime Maximum allowed uptime (otherwise, pause before launching the next process). Negative means don't care.\n"; + print "\tsleepTime Number of seconds to sleep after running a process (zero means no sleep)\n"; + print "\tfile File containing all commands to be executed (one per line)\n"; + exit(10); +} + +#--- +# Read file and launch processes +#--- +my($cmd); +my($startTime) = time(); +my($numProc) = 0; +open BATCH, $file; +while( $cmd = <BATCH> ) { + chomp $cmd; + + # Can we launch more processes? + if( $numProc < $maxNumProc ) { + + my( $run ) = 0; + + do { + # Should the next process run now? (don't run if CPU is too high) + if( shouldRun() ) { + my $retFork = fork(); + $run = 1; + + if( $retFork == 0 ) { # Child process + # Redirect STDOUT and STDERR to files + open STDOUT, '>', "$$.stdout" or die "Can't redirect STDOUT (PID=$$): $!"; + open STDERR, '>', "$$.stderr" or die "Can't redirect STDERR (PID=$$): $!"; + exec($cmd); + } elsif ($retFork == '' ) { # Error launching process + print STDERR "Error launching process:\t'$cmd'\n"; + } else { + printLog("Executing (PID=$retFork):\t'$cmd'"); + $numProc++; + } + } else { printLog("No running"); } + + # Sleep before next process + if( $sleepTime > 0 ) { + printLog "Sleep $sleepTime seconds"; + sleep($sleepTime); + } + } while( ! $run ); + } + + # Number of processes exceded? => Wait until one finishes + if( $numProc >= $maxNumProc ) { + # Wait for processes to die + my $deadPid = wait(); + printLog "Process PID=$deadPid finished."; + $numProc--; + if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } + } +} + +#--- +# Done, wait for the remining processes to die +#--- +my($deadPid); +while( ($deadPid = wait()) >= 0 ) { # Wait for processes to die + $numProc--; + my($now) = localtime(); + printLog "Process PID=$deadPid finished."; + if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } +} + +my($elapsed) = time() - $startTime; +print "All processes finished.\nElapsed time $elapsed seconds.\n"; + +close BATCH; + |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_build.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_build.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,3 @@ +#!/bin/sh + +./scripts/queue.pl 22 24 15 ./scripts/queue_build.txt |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_build.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_build.txt Fri Apr 20 11:22:59 2012 -0400 |
| b |
| b'@@ -0,0 +1,387 @@\n+./scripts/snpEffXL.sh build -v anoCar1.0.60\n+./scripts/snpEffXL.sh build -v btau4.0.59\n+./scripts/snpEffXL.sh build -v btau4.0.60\n+./scripts/snpEffXL.sh build -v bushBaby1.60\n+./scripts/snpEffXL.sh build -v calJac3.2.1.60\n+./scripts/snpEffXL.sh build -v canFam2.59\n+./scripts/snpEffXL.sh build -v canFam2.60\n+./scripts/snpEffXL.sh build -v cat1.60\n+./scripts/snpEffXL.sh build -v cavPor3.60\n+./scripts/snpEffXL.sh build -v ce.WS210.60\n+./scripts/snpEffXL.sh build -v chimp2.1.59\n+./scripts/snpEffXL.sh build -v chimp2.1.60\n+./scripts/snpEffXL.sh build -v choHof1.60\n+./scripts/snpEffXL.sh build -v cInt2.60\n+./scripts/snpEffXL.sh build -v cSav2.0.60\n+./scripts/snpEffXL.sh build -v danRer8.59\n+./scripts/snpEffXL.sh build -v danRer9.60\n+./scripts/snpEffXL.sh build -v dasNov2.60\n+./scripts/snpEffXL.sh build -v dipOrd1.60\n+./scripts/snpEffXL.sh build -v dm5.25.59\n+./scripts/snpEffXL.sh build -v dm5.25.60\n+./scripts/snpEffXL.sh build -v 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kw1407.2012\n+./scripts/snpEffXL.sh build -v -gff3 kw1407.2012\n+./scripts/snpEffXL.sh build -v -gff3 maizeZmB73\n+./scripts/snpEffXL.sh build -v -gff3 mmm.2012\n+./scripts/snpEffXL.sh build -v'..b'uild -v -gtf22 pteVam1.63\n+./scripts/snpEffXL.sh build -v -gtf22 pteVam1.64\n+./scripts/snpEffXL.sh build -v -gtf22 pteVam1.65\n+./scripts/snpEffXL.sh build -v -gtf22 pteVam1.66\n+./scripts/snpEffXL.sh build -v -gtf22 rat3.4.61\n+./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.63\n+./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.64\n+./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.65\n+./scripts/snpEffXL.sh build -v -gtf22 RGSC3.4.66\n+./scripts/snpEffXL.sh build -v -gtf22 sacCer2.61\n+./scripts/snpEffXL.sh build -v -gtf22 sorAra1.61\n+./scripts/snpEffXL.sh build -v -gtf22 speTri1.61\n+./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.63\n+./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.64\n+./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.65\n+./scripts/snpEffXL.sh build -v -gtf22 SQUIRREL.66\n+./scripts/snpEffXL.sh build -v -gtf22 sScrofa9.61\n+./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.63\n+./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.64\n+./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.65\n+./scripts/snpEffXL.sh build -v -gtf22 Sscrofa9.66\n+./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.61\n+./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.63\n+./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.64\n+./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.65\n+./scripts/snpEffXL.sh build -v -gtf22 taeGut3.2.4.66\n+./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.61\n+./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.63\n+./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.64\n+./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.65\n+./scripts/snpEffXL.sh build -v -gtf22 tarSyr1.66\n+./scripts/snpEffXL.sh build -v -gtf22 tenrec1.61\n+./scripts/snpEffXL.sh build -v -gtf22 TENREC.63\n+./scripts/snpEffXL.sh build -v -gtf22 TENREC.64\n+./scripts/snpEffXL.sh build -v -gtf22 TENREC.65\n+./scripts/snpEffXL.sh build -v -gtf22 TENREC.66\n+./scripts/snpEffXL.sh build -v -gtf22 test_ENSG00000158062\n+./scripts/snpEffXL.sh build -v -gtf22 testHg3763ChrY\n+./scripts/snpEffXL.sh build -v -gtf22 tetraodon8.61\n+./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.63\n+./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.64\n+./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.65\n+./scripts/snpEffXL.sh build -v -gtf22 TETRAODON8.66\n+./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.63\n+./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.64\n+./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.65\n+./scripts/snpEffXL.sh build -v -gtf22 TREESHREW.66\n+./scripts/snpEffXL.sh build -v -gtf22 tupBel1.61\n+./scripts/snpEffXL.sh build -v -gtf22 turkey.UMD2.61\n+./scripts/snpEffXL.sh build -v -gtf22 turTru1.61\n+./scripts/snpEffXL.sh build -v -gtf22 turTru1.63\n+./scripts/snpEffXL.sh build -v -gtf22 turTru1.64\n+./scripts/snpEffXL.sh build -v -gtf22 turTru1.65\n+./scripts/snpEffXL.sh build -v -gtf22 turTru1.66\n+./scripts/snpEffXL.sh build -v -gtf22 UMD2.63\n+./scripts/snpEffXL.sh build -v -gtf22 UMD2.64\n+./scripts/snpEffXL.sh build -v -gtf22 UMD2.65\n+./scripts/snpEffXL.sh build -v -gtf22 UMD2.66\n+./scripts/snpEffXL.sh build -v -gtf22 UMD3_1\n+./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.64\n+./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.65\n+./scripts/snpEffXL.sh build -v -gtf22 UMD3.1.66\n+./scripts/snpEffXL.sh build -v -gtf22 vicPac1.61\n+./scripts/snpEffXL.sh build -v -gtf22 vicPac1.63\n+./scripts/snpEffXL.sh build -v -gtf22 vicPac1.64\n+./scripts/snpEffXL.sh build -v -gtf22 vicPac1.65\n+./scripts/snpEffXL.sh build -v -gtf22 vicPac1.66\n+./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.63\n+./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.64\n+./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.65\n+./scripts/snpEffXL.sh build -v -gtf22 WASHUC2.66\n+./scripts/snpEffXL.sh build -v -gtf22 WS220.63\n+./scripts/snpEffXL.sh build -v -gtf22 WS220.64\n+./scripts/snpEffXL.sh build -v -gtf22 WS220.65\n+./scripts/snpEffXL.sh build -v -gtf22 WS220.66\n+./scripts/snpEffXL.sh build -v -gtf22 xtrop4.1.61\n+./scripts/snpEffXL.sh build -v -gtf22 Zv9.63\n+./scripts/snpEffXL.sh build -v -gtf22 Zv9.64\n+./scripts/snpEffXL.sh build -v -gtf22 Zv9.65\n+./scripts/snpEffXL.sh build -v -gtf22 Zv9.66\n' |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_build_regulation.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_build_regulation.txt Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,73 @@ +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Nuclei GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Kidney GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Liver GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Anterior_Caudate GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Cingulate_Gyrus GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Hippocampus_Middle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Inferior_Temporal_Lobe GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Mid_Frontal_Lobe GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Substantia_Nigra GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Luminal_Epithelial_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Myoepithelial_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Stem_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_vHMEC GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD15_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD19_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD3_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Memory_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Naive_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD56_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Naive_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Colonic_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Duodenum_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-I3 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-WA7 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Adrenal_Gland GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Brain GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Heart GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Large GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Small GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Left GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Right GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Left GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Right GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Thymus GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H1 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H3K9me3 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H9 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES48 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES6 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES64 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType IMR90 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType input GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-11a GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-15b GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-18c GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-20b GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_19 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_4 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_6 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD34_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD56_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Muscle_Satellite_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Cortex_Derived GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Pancreatic_Islets GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Penis_Foreskin_Keratinocyte_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Peripheral_Blood_Mononuclear_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Smooth_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Skeletal_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Stomach_Smooth_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Th17_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Treg_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType uniques GRCh37.64 |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_dump.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_dump.txt Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,137 @@ +./scripts/snpEff.sh dump agam > agam.dump +./scripts/snpEff.sh dump ailmel1.61 > ailmel1.61.dump +./scripts/snpEff.sh dump alyrata107 > alyrata107.dump +./scripts/snpEff.sh dump alyrata107 > alyrata107.dump +./scripts/snpEff.sh dump amel2 > amel2.dump +./scripts/snpEff.sh dump anoCar1.0.60 > anoCar1.0.60.dump +./scripts/snpEff.sh dump anoCar2.0.61 > anoCar2.0.61.dump +./scripts/snpEff.sh dump aquiCoer > aquiCoer.dump +./scripts/snpEff.sh dump athaliana130 > athaliana130.dump +./scripts/snpEff.sh dump btau4.0.59 > btau4.0.59.dump +./scripts/snpEff.sh dump btau4.0.60 > btau4.0.60.dump +./scripts/snpEff.sh dump btau4.0.61 > btau4.0.61.dump +./scripts/snpEff.sh dump bushBaby1.60 > bushBaby1.60.dump +./scripts/snpEff.sh dump bushBaby1.61 > bushBaby1.61.dump +./scripts/snpEff.sh dump calJac3.2.1.60 > calJac3.2.1.60.dump +./scripts/snpEff.sh dump calJac3.2.1.61 > calJac3.2.1.61.dump +./scripts/snpEff.sh dump canFam2.59 > canFam2.59.dump +./scripts/snpEff.sh dump canFam2.60 > canFam2.60.dump +./scripts/snpEff.sh dump canFam2.61 > canFam2.61.dump +./scripts/snpEff.sh dump cat1.60 > cat1.60.dump +./scripts/snpEff.sh dump cat1.61 > cat1.61.dump +./scripts/snpEff.sh dump cavPor3.60 > cavPor3.60.dump +./scripts/snpEff.sh dump cavPor3.61 > cavPor3.61.dump +./scripts/snpEff.sh dump ce.WS210.60 > ce.WS210.60.dump +./scripts/snpEff.sh dump ce.WS220.61 > ce.WS220.61.dump +./scripts/snpEff.sh dump chimp2.1.59 > chimp2.1.59.dump +./scripts/snpEff.sh dump chimp2.1.60 > chimp2.1.60.dump +./scripts/snpEff.sh dump chimp2.1.61 > chimp2.1.61.dump +./scripts/snpEff.sh dump choHof1.60 > choHof1.60.dump +./scripts/snpEff.sh dump choHof1.61 > choHof1.61.dump +./scripts/snpEff.sh dump cInt2.60 > cInt2.60.dump +./scripts/snpEff.sh dump cInt2.61 > cInt2.61.dump +./scripts/snpEff.sh dump cSav2.0.60 > cSav2.0.60.dump +./scripts/snpEff.sh dump cSav2.0.61 > cSav2.0.61.dump +./scripts/snpEff.sh dump danRer6 > danRer6.dump +./scripts/snpEff.sh dump danRer8.59 > danRer8.59.dump +./scripts/snpEff.sh dump danRer9.60 > danRer9.60.dump +./scripts/snpEff.sh dump danRer9.61 > danRer9.61.dump +./scripts/snpEff.sh dump dasNov2.60 > dasNov2.60.dump +./scripts/snpEff.sh dump dasNov2.61 > dasNov2.61.dump +./scripts/snpEff.sh dump dipOrd1.60 > dipOrd1.60.dump +./scripts/snpEff.sh dump dipOrd1.61 > dipOrd1.61.dump +./scripts/snpEff.sh dump dm5.12 > dm5.12.dump +./scripts/snpEff.sh dump dm5.22 > dm5.22.dump +./scripts/snpEff.sh dump dm5.25.59 > dm5.25.59.dump +./scripts/snpEff.sh dump dm5.25.60 > dm5.25.60.dump +./scripts/snpEff.sh dump dm5.25.61 > dm5.25.61.dump +./scripts/snpEff.sh dump dm5.30 > dm5.30.dump +./scripts/snpEff.sh dump dm5.31 > dm5.31.dump +./scripts/snpEff.sh dump dm5.32 > dm5.32.dump +./scripts/snpEff.sh dump dm5.34 > dm5.34.dump +./scripts/snpEff.sh dump equCab2.60 > equCab2.60.dump +./scripts/snpEff.sh dump equCab2.61 > equCab2.61.dump +./scripts/snpEff.sh dump eriEur1.60 > eriEur1.60.dump +./scripts/snpEff.sh dump eriEur1.61 > eriEur1.61.dump +./scripts/snpEff.sh dump fugu4.60 > fugu4.60.dump +./scripts/snpEff.sh dump fugu4.61 > fugu4.61.dump +./scripts/snpEff.sh dump gacu1.60 > gacu1.60.dump +./scripts/snpEff.sh dump gacu1.61 > gacu1.61.dump +./scripts/snpEff.sh dump ggallus2.59 > ggallus2.59.dump +./scripts/snpEff.sh dump ggallus2.60 > ggallus2.60.dump +./scripts/snpEff.sh dump ggallus2.61 > ggallus2.61.dump +./scripts/snpEff.sh dump gorGor3.60 > gorGor3.60.dump +./scripts/snpEff.sh dump gorGor3.61 > gorGor3.61.dump +./scripts/snpEff.sh dump hg36.54 > hg36.54.dump +./scripts/snpEff.sh dump hg37.59 > hg37.59.dump +./scripts/snpEff.sh dump hg37.60 > hg37.60.dump +./scripts/snpEff.sh dump hg37.61 > hg37.61.dump +./scripts/snpEff.sh dump hg37 > hg37.dump +./scripts/snpEff.sh dump hiv > hiv.dump +./scripts/snpEff.sh dump loxAfr3.60 > loxAfr3.60.dump +./scripts/snpEff.sh dump loxAfr3.61 > loxAfr3.61.dump +./scripts/snpEff.sh dump medaka1.60 > medaka1.60.dump +./scripts/snpEff.sh dump medaka1.61 > medaka1.61.dump +./scripts/snpEff.sh dump meug1.0.60 > meug1.0.60.dump +./scripts/snpEff.sh dump meug1.0.61 > meug1.0.61.dump +./scripts/snpEff.sh dump micMur1.60 > micMur1.60.dump +./scripts/snpEff.sh dump micMur1.61 > micMur1.61.dump +./scripts/snpEff.sh dump mm37.59 > mm37.59.dump +./scripts/snpEff.sh dump mm37.60 > mm37.60.dump +./scripts/snpEff.sh dump mm37.61 > mm37.61.dump +./scripts/snpEff.sh dump mm37 > mm37.dump +./scripts/snpEff.sh dump mmul1.60 > mmul1.60.dump +./scripts/snpEff.sh dump mmul1.61 > mmul1.61.dump +./scripts/snpEff.sh dump monDom5.60 > monDom5.60.dump +./scripts/snpEff.sh dump monDom5.61 > monDom5.61.dump +./scripts/snpEff.sh dump myoLuc1.60 > myoLuc1.60.dump +./scripts/snpEff.sh dump myoLuc1.61 > myoLuc1.61.dump +./scripts/snpEff.sh dump oana5.60 > oana5.60.dump +./scripts/snpEff.sh dump oana5.61 > oana5.61.dump +./scripts/snpEff.sh dump ochPri2.60 > ochPri2.60.dump +./scripts/snpEff.sh dump ochPri2.61 > ochPri2.61.dump +./scripts/snpEff.sh dump oryCun2.60 > oryCun2.60.dump +./scripts/snpEff.sh dump oryCun2.61 > oryCun2.61.dump +./scripts/snpEff.sh dump paeru.PA01 > paeru.PA01.dump +./scripts/snpEff.sh dump paeru.PA14 > paeru.PA14.dump +./scripts/snpEff.sh dump pfluo.SBW25.NC_009444 > pfluo.SBW25.NC_009444.dump +./scripts/snpEff.sh dump pfluo.SBW25.NC_012660 > pfluo.SBW25.NC_012660.dump +./scripts/snpEff.sh dump ppyg2.60 > ppyg2.60.dump +./scripts/snpEff.sh dump ppyg2.61 > ppyg2.61.dump +./scripts/snpEff.sh dump proCap1.60 > proCap1.60.dump +./scripts/snpEff.sh dump proCap1.61 > proCap1.61.dump +./scripts/snpEff.sh dump pteVam1.60 > pteVam1.60.dump +./scripts/snpEff.sh dump pteVam1.61 > pteVam1.61.dump +./scripts/snpEff.sh dump rat3.4.59 > rat3.4.59.dump +./scripts/snpEff.sh dump rat3.4.60 > rat3.4.60.dump +./scripts/snpEff.sh dump rat3.4.61 > rat3.4.61.dump +./scripts/snpEff.sh dump sacCer2.59 > sacCer2.59.dump +./scripts/snpEff.sh dump sacCer2.60 > sacCer2.60.dump +./scripts/snpEff.sh dump sacCer2.61 > sacCer2.61.dump +./scripts/snpEff.sh dump sacCer2 > sacCer2.dump +./scripts/snpEff.sh dump SIVmac239 > SIVmac239.dump +./scripts/snpEff.sh dump sorAra1.60 > sorAra1.60.dump +./scripts/snpEff.sh dump sorAra1.61 > sorAra1.61.dump +./scripts/snpEff.sh dump speTri1.60 > speTri1.60.dump +./scripts/snpEff.sh dump speTri1.61 > speTri1.61.dump +./scripts/snpEff.sh dump sScrofa9.60 > sScrofa9.60.dump +./scripts/snpEff.sh dump sScrofa9.61 > sScrofa9.61.dump +./scripts/snpEff.sh dump taeGut3.2.4.60 > taeGut3.2.4.60.dump +./scripts/snpEff.sh dump taeGut3.2.4.61 > taeGut3.2.4.61.dump +./scripts/snpEff.sh dump tarSyr1.60 > tarSyr1.60.dump +./scripts/snpEff.sh dump tarSyr1.61 > tarSyr1.61.dump +./scripts/snpEff.sh dump tenrec1.60 > tenrec1.60.dump +./scripts/snpEff.sh dump tenrec1.61 > tenrec1.61.dump +./scripts/snpEff.sh dump testCase > testCase.dump +./scripts/snpEff.sh dump tetraodon8.60 > tetraodon8.60.dump +./scripts/snpEff.sh dump tetraodon8.61 > tetraodon8.61.dump +./scripts/snpEff.sh dump tupBel1.60 > tupBel1.60.dump +./scripts/snpEff.sh dump tupBel1.61 > tupBel1.61.dump +./scripts/snpEff.sh dump turkey.UMD2.61 > turkey.UMD2.61.dump +./scripts/snpEff.sh dump turTru1.60 > turTru1.60.dump +./scripts/snpEff.sh dump turTru1.61 > turTru1.61.dump +./scripts/snpEff.sh dump vacwr > vacwr.dump +./scripts/snpEff.sh dump vicPac1.60 > vicPac1.60.dump +./scripts/snpEff.sh dump vicPac1.61 > vicPac1.61.dump +./scripts/snpEff.sh dump xtrop4.1.60 > xtrop4.1.60.dump +./scripts/snpEff.sh dump xtrop4.1.61 > xtrop4.1.61.dump |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_test.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,3 @@ +#!/bin/sh + +./scripts/queue.pl 22 24 15 ./scripts/queue_test.txt |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/queue_test.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/queue_test.txt Fri Apr 20 11:22:59 2012 -0400 |
| b |
| b'@@ -0,0 +1,231 @@\n+./scripts/snpEffXL.sh cds -v ailmel1.61 data/ailmel1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v ailMel1.63 data/ailMel1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v ailMel1.64 data/ailMel1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v anoCar1.0.60 data/anoCar1.0.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v anoCar2.0.61 data/anoCar2.0.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v AnoCar2.0.63 data/AnoCar2.0.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v AnoCar2.0.64 data/AnoCar2.0.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BDGP5.25.63 data/BDGP5.25.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BDGP5.25.64 data/BDGP5.25.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADD2.63 data/BROADD2.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADD2.64 data/BROADD2.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADO5.63 data/BROADO5.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADO5.64 data/BROADO5.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADS1.63 data/BROADS1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BROADS1.64 data/BROADS1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v btau4.0.59 data/btau4.0.59/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v btau4.0.60 data/btau4.0.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v btau4.0.61 data/btau4.0.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v Btau_4.0.63 data/Btau_4.0.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v bushBaby1.60 data/bushBaby1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v bushBaby1.61 data/bushBaby1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BUSHBABY1.63 data/BUSHBABY1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v BUSHBABY1.64 data/BUSHBABY1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v calJac3.2.1.60 data/calJac3.2.1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v calJac3.2.1.61 data/calJac3.2.1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v canFam2.59 data/canFam2.59/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v canFam2.60 data/canFam2.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v canFam2.61 data/canFam2.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cat1.60 data/cat1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v cat1.61 data/cat1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CAT.63 data/CAT.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CAT.64 data/CAT.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cavPor3.60 data/cavPor3.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v cavPor3.61 data/cavPor3.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cavPor3.63 data/cavPor3.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cavPor3.64 data/cavPor3.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v ce.WS210.60 data/ce.WS210.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v ce.WS220.61 data/ce.WS220.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v chimp2.1.59 data/chimp2.1.59/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v chimp2.1.60 data/chimp2.1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v chimp2.1.61 data/chimp2.1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CHIMP2.1.63 data/CHIMP2.1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CHIMP2.1.64 data/CHIMP2.1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v choHof1.60 data/choHof1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v choHof1.61 data/choHof1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v choHof1.63 data/choHof1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v choHof1.64 data/choHof1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cInt2.60 data/cInt2.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v cInt2.61 data/cInt2.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.63 data/C_jacchus3.2.1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.64 data/C_jacchus3.2.1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v COMMON_SHREW1.63 data/COMMON_SHREW1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v COMMON_SHREW1.64 data/COMMON_SHREW1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v cSav2.0.60 data/cSav2.0.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v cSav2.0.61 data/cSav2.0.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CSAV2.0.63 data/CSAV2.0.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v CSAV2.0.64 data/CSAV2.0.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v danRer8.59 data/danRer8.59/cds.tx'..b'/scripts/snpEffXL.sh cds -v rat3.4.60 data/rat3.4.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v rat3.4.61 data/rat3.4.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v RGSC3.4.63 data/RGSC3.4.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v RGSC3.4.64 data/RGSC3.4.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v sacCer2.59 data/sacCer2.59/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v sacCer2.60 data/sacCer2.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v sacCer2.61 data/sacCer2.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v sacCer2 data/sacCer2/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v sorAra1.60 data/sorAra1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v sorAra1.61 data/sorAra1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v speTri1.60 data/speTri1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v speTri1.61 data/speTri1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v SQUIRREL.63 data/SQUIRREL.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v SQUIRREL.64 data/SQUIRREL.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v sScrofa9.60 data/sScrofa9.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v sScrofa9.61 data/sScrofa9.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v Sscrofa9.63 data/Sscrofa9.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v Sscrofa9.64 data/Sscrofa9.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v taeGut3.2.4.60 data/taeGut3.2.4.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v taeGut3.2.4.61 data/taeGut3.2.4.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v taeGut3.2.4.63 data/taeGut3.2.4.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v taeGut3.2.4.64 data/taeGut3.2.4.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v tarSyr1.60 data/tarSyr1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v tarSyr1.61 data/tarSyr1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v tarSyr1.63 data/tarSyr1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v tarSyr1.64 data/tarSyr1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v tenrec1.60 data/tenrec1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v tenrec1.61 data/tenrec1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TENREC.63 data/TENREC.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TENREC.64 data/TENREC.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v testCase data/testCase/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v tetraodon8.60 data/tetraodon8.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v tetraodon8.61 data/tetraodon8.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TETRAODON8.63 data/TETRAODON8.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TETRAODON8.64 data/TETRAODON8.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TREESHREW.63 data/TREESHREW.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v TREESHREW.64 data/TREESHREW.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v tupBel1.60 data/tupBel1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v tupBel1.61 data/tupBel1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v turkey.UMD2.61 data/turkey.UMD2.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v turTru1.60 data/turTru1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v turTru1.61 data/turTru1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v turTru1.63 data/turTru1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v turTru1.64 data/turTru1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v UMD2.63 data/UMD2.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v UMD2.64 data/UMD2.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v UMD3.1.64 data/UMD3.1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v vicPac1.60 data/vicPac1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v vicPac1.61 data/vicPac1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v vicPac1.63 data/vicPac1.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v vicPac1.64 data/vicPac1.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v WASHUC2.63 data/WASHUC2.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v WASHUC2.64 data/WASHUC2.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v WS220.63 data/WS220.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v WS220.64 data/WS220.64/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v xtrop4.1.60 data/xtrop4.1.60/cds.txt.gz\n+./scripts/snpEffXL.sh cds -v xtrop4.1.61 data/xtrop4.1.61/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v Zv9.63 data/Zv9.63/cds.fa.gz\n+./scripts/snpEffXL.sh cds -v Zv9.64 data/Zv9.64/cds.fa.gz\n' |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/randBedIntervals.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/randBedIntervals.pl Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,36 @@ +#!/usr/bin/perl + +# Number of intervals per chromosome +$intsPerChr = 10; + +# Max interval len +$maxLen = 1000; + +# Chromosome length +$len{'chr2L'} = 23299195; +$len{'chr2LHet'} = 373492; +$len{'chr2R'} = 21411048; +$len{'chr2RHet'} = 3329880; +$len{'chr3L'} = 24850358; +$len{'chr3LHet'} = 2587444; +$len{'chr3R'} = 28253873; +$len{'chr3RHet'} = 2548985; +$len{'chr4'} = 1368761; +$len{'chrdmel_mitochondrion_genome'} = 19790; +$len{'chrUextra'} = 29367225; +$len{'chrU'} = 10174655; +$len{'chrX'} = 22703118; +$len{'chrXHet'} = 206671; +$len{'chrYHet'} = 351384; + +foreach $chr ( sort keys %len ) { + $max = $len{$chr} - $maxLen - 1000; + + for( $i=0 ; $i < $intsPerChr ; $i++ ) { + $start = int( rand() * $max ); + $end = int( rand() * $maxLen ) + $start; + + print "$chr\t$start\t$end\n"; + } +} + |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.pl Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#!/usr/bin/perl + + +print "##INFO=<ID=SIFT_SCORE,Number=1,Type=Float,Description=\"SIFT score, 0 = Damaging, 1=Tolerated\">\n"; +print "##INFO=<ID=SIFT_CONS,Number=1,Type=Float,Description=\"SIFT median conservation value, as log2. 0=High confidence, 4.32=Low confidence\">\n"; +print "##INFO=<ID=SIFT_SEQS,Number=1,Type=Integer,Description=\"SIFT number of sequences at position\">\n"; +print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"; + +while( $l = <STDIN> ) { + chomp $l; + ($chr, $coord1, $nt1, $nt2, $score, $median, $seqs_rep) = split /\t/, $l; + + # Trim spaces + if( $seqs_rep =~ /\s(.*)/ ) { $seqs_rep = $1; } + + $coord1++; # Get it in one-based coordinates + + print "$chr\t$coord1\t.\t$nt1\t$nt2\t.\t.\tSIFT_SCORE=$score;SIFT_CONS=$median;SIFT_SEQS=$seqs_rep\n"; +} |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/sift2vcf.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,47 @@ +#!/bin/sh -e + +SQLITE=$HOME/tools/sqlite3 +SQLITE=sqlite3 +OUT_FILE="sift.txt" +OUT_SORT_FILE="sift.sort.txt" +OUT_VCF="sift.vcf" + +# Download files +for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sqlite.gz Human_CHR17.sqlite.gz Human_CHR18.sqlite.gz Human_CHR19.sqlite.gz Human_CHR2.sqlite.gz Human_CHR20.sqlite.gz Human_CHR21.sqlite.gz Human_CHR22.sqlite.gz Human_CHR3.sqlite.gz Human_CHR4.sqlite.gz Human_CHR5.sqlite.gz Human_CHR6.sqlite.gz Human_CHR7.sqlite.gz Human_CHR8.sqlite.gz Human_CHR9.sqlite.gz Human_CHRX.sqlite.gz Human_CHRY.sqlite.gz Human_Supp.sqlite.gz Human_enst.sqlite.gz +do + url=ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/$f + echo Getting file $url + #wget $url +done + +# Unzip files +for f in Human_CHR*.sqlite.gz +do + echo Decompressing file $f + #gunzip $f +done + +# Dumping data +rm -f $OUT_FILE +for f in Human_CHR*.sqlite +do + echo Dumping Database $f to $OUT_FILE + + TABLES=`$SQLITE $f ".tables" | tr "\n" "\t"` + for t in $TABLES + do + echo " Dumping Table $t" + + $SQLITE $f "select CHR, COORD1, NT1, NT2, SCORE, MEDIAN, SEQS_REP from $t where SCORE != '' AND NT1 != NT2;" \ + | tr "|" "\t" \ + | sed "s/^chr//" \ + >> $OUT_FILE + done +done + +echo Sorting file +sort -k 1 -n -k 2 -n -o $OUT_SORT_FILE $OUT_FILE + +echo Creating VCF +cat $OUT_SORT_FILE | sift2vcf.pl > $OUT_VCF + |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/smoothScatter.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/smoothScatter.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,82 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a smooth scatter plot +# Data is feed as two column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'smoothScatter'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R table +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\ty\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + ($x, $y) = split /\t/, $l; + + # Does the string contain exactly one number? (can be float) + if(( $x =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) && ( $y =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ )) { print TXT "$x\t$y\n"; } +} +close TXT; + +#--- +# Create an R program, save histogram plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +smoothLowess <- function( x, y, title, q=1.0 ) { + # Show only this part of the data + xmin <- quantile( x, 1-q ) + xmax <- quantile( x, q ) + + ymin <- quantile( y, 1-q ) + ymax <- quantile( y, q ) + + keep <- (x >= xmin) & (x <= xmax) & (y >= ymin) & (y <= ymax); + qx <- x[ keep ] + qy <- y[ keep ] + + smoothScatter(qx, qy, main=title, ylab='Y (column 2)', xlab='X (column 1)'); + lines( lowess(qx,qy), col='orange' ); +} + +png('$pngFile', width = 1024, height = 1024); +par( mfrow=c(2,1) ); + +data <- read.csv("$txtFile", sep='\\t', header = TRUE); +x <- data\$x +y <- data\$y + +smoothLowess(x, y, "Smooth scatter plot and Lowess", 1.0); +smoothLowess(x, y, "Smooth scatter plot and Lowess: Quantile [2% - 98%]", 0.98); + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; + |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/snpEff.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/snpEff.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +LIB=$HOME/snpEff/lib + +java -Xmx1G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $* |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/snpEffM.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/snpEffM.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff +LIB=$HOME/snpEff/lib + +java -Xmx3G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $* |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/snpEffXL.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/snpEffXL.sh Fri Apr 20 11:22:59 2012 -0400 |
| b |
| @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +LIB=$HOME/snpEff/lib + +java -Xmx20G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $* |
| b |
| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/snpSift.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/snpSift.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,15 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/ +LIB=$HOME/snpEff/lib +LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/ + +# Old library reference: +# -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR:$DIR_SNPSIFT" \ + +java -Xmx1G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$LIB_SNPSIFT/antlr-3.4-complete.jar:$DIR:$DIR_SNPSIFT" \ + ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \ + $* + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,25 @@ +#!/bin/sh + +REF=GRCh37.66 + +IN_VCF=$HOME/snpEff/1kg/test.Broad_NS_SYN.vcf.gz +OUT_VCF=all.vcf + +# Run SnpEff +./scripts/snpEffXL.sh eff -v -noStats -o vcf $REF $IN_VCF > $OUT_VCF + +# Calculate number of lines +SILENT=`cat $OUT_VCF | grep "SILENT" | wc -l` +MISSENSE=`cat $OUT_VCF | grep "MISSENSE" | wc -l` +NONSENSE=`cat $OUT_VCF | grep "NONSENSE" | wc -l` +SILENT_AND_MISSENSE=`cat $OUT_VCF | grep "SILENT" | grep "MISSENSE" | wc -l` + +PSILENT=`echo "100 * $SILENT/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` +PMISSENSE=`echo "100 * $MISSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` +PNONSENSE=`echo "100 * $NONSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` + +echo -e "Silent :\t$SILENT ($PSILENT %)" +echo -e "Missense :\t$MISSENSE ($PMISSENSE %)" +echo -e "Nonsense :\t$NONSENSE ($PNONSENSE %)" +echo -e "Silent and missense :\t$SILENT_AND_MISSENSE" + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/uniqCount.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/uniqCount.pl Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,13 @@ +#!/usr/bin/perl + +while( $l = <STDIN> ) { + chomp $l; + $count{$l}++; +} + +$tot = 0; +foreach $key ( sort keys %count ) { + print "$count{$key}\t$key\n"; + $tot += $count{$key}; +} +print "$tot\tTotal\n"; |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/vcfEffOnePerLine.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/vcfEffOnePerLine.pl Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| @@ -0,0 +1,53 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Read a VCF file (via STDIN), split EFF fields from INFO column into many lines +# leaving one line per effect. +# +# Note: In lines having multiple effects, all other information will be +# repeated. Only the 'EFF' field will change. +# +# Pablo Cingolani 2012 +#------------------------------------------------------------------------------- + +$INFO_FIELD_NUM = 7; + +while( $l = <STDIN> ) { + # Show header lines + if( $l =~ /^#/ ) { print $l; } + else { + chomp $l; + + @t = @infos = @effs = (); # Clear arrays + + # Non-header lines: Parse fields + @t = split /\t/, $l; + + # Get INFO column + $info = $t[ $INFO_FIELD_NUM ]; + + # Parse INFO column + @infos = split /;/, $info; + + # Find EFF field + $infStr = ""; + foreach $inf ( @infos ) { + # Is this the EFF field? => Find it and split it + if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; } + else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; } + } + + # Print VCF line + if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line + else { + $pre = ""; + for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; } + + $post = ""; + for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; } + + foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; } + } + } +} |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/scripts/vcfSpeedTest.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/vcfSpeedTest.sh Fri Apr 20 11:22:59 2012 -0400 |
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| @@ -0,0 +1,8 @@ +#!/bin/sh + +for testNum in 1 2 3 4 +do + ./scripts/snpEffM.sh test $testNum test.1M.vcf > test.1M.out.vcf + echo +done + |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/snpEff.config --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/snpEff.config Fri Apr 20 11:22:59 2012 -0400 |
| [ |
| b"@@ -0,0 +1,1160 @@\n+\n+#-------------------------------------------------------------------------------\n+#\n+# SnpEff configuration file\n+#\n+#\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tPablo Cingolani\n+#-------------------------------------------------------------------------------\n+\n+#---\n+# Databases are stored here\n+# E.g.: Information for 'hg19' is stored in data_dir/hg19/\n+#\n+# Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory\n+#---\n+data_dir = ~/snpEff/data/\n+\n+#---\n+# Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')\n+#---\n+database_repository = http://downloads.sourceforge.net/project/snpeff/databases\n+\n+#-------------------------------------------------------------------------------\n+# Genomes\n+#\n+# One entry per genome version. \n+#\n+# For genome version 'ZZZ' the entries look like\n+#\tZZZ.genome : Real name for ZZZ (e.g. 'Human')\n+#\tZZZ.reference : [Optional] Comma separated list of URL to site/s where information for building ZZZ database was extracted.\n+#\tZZZ.chrName.codonTable : [Optional] Define codon table used for chromosome 'chrName' (Default: 'codon.Standard')\n+#\n+#-------------------------------------------------------------------------------\n+\n+# Ailuropoda_melanoleuca\n+ailmel1.61.genome : Ailuropoda_melanoleuca\n+\n+# Anopheles_gambiae\n+agam.genome : Anopheles_gambiae\n+agam.reference : http://agambiae.vectorbase.org/GetData/ \n+\n+agam2.6.genome : Anopheles_gambiae\n+agam2.6.reference : http://agambiae.vectorbase.org/GetData/ \n+\n+# Arabidopsis lyrata\n+alyrata107.genome : Arabidopsis_lyrata\n+alyrata107.reference : http://www.phytozome.net/search.php?method=Org_Alyrata\n+\n+alyrata1.genome : Arabidopsis_lyrata\n+alyrata1.reference : http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html\n+\n+# Apis mellifera\n+amel2.genome : Bee\n+amel2.reference : http://beebase.org\n+\n+# Anolis carolinensis genes (AnoCar1.0) (ENSEMBL)\n+anoCar1.0.60.genome : Anolis_carolinensis\n+anoCar2.0.61.genome : Anolis_carolinensis\n+\n+# Aquilegia coerulea\n+aquiCoer.genome : Aquilegia_coerulea\n+\n+# Arabidopsis Thaliana\n+athaliana130.genome : Arabidopsis_Thaliana\n+athaliana130.reference : http://www.phytozome.net/dataUsagePolicy.php?org=Org_Athaliana\n+\n+athalianaTair9.genome : Arabidopsis_Thaliana\n+athalianaTair9.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release\n+\n+athalianaTair10.genome : Arabidopsis_Thaliana\n+athalianaTair10.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release\n+\n+# Bos taurus genes (Btau_4.0) (ENSEMBL)\n+btau4.0.59.genome : Bos_taurus\n+btau4.0.60.genome : Bos_taurus\n+btau4.0.61.genome : Bos_taurus\n+\n+# Otolemur garnettii genes (otoGar1) (ENSEMBL)\n+bushBaby1.60.genome : Otolemur_garnettii\n+bushBaby1.61.genome : Otolemur_garnettii\n+\n+# Candida_albicans_SC5314 \n+cAlbicansv21.genome: Candida_albicans_SC5314\n+cAlbicansv21.reference: http://www.candidagenome.org/download/gff/C_albicans_SC5314/\n+\n+# C. Briggsae \n+c_briggsae_WS230.genome : Caenorhabditis_briggsae\n+c_briggsae_WS230.reference : ftp://ftp.wormbase.org/pub/wormbase/releases/WS230/species/c_briggsae/\n+\n+# Cryptococcus neoformans\n+c_neoformans.genome: Cryptococcus_neoformans\n+c_neoformans.reference: http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiDownloads.html\n+\n+# Callithrix jacchus genes (calJac3) (ENSEMBL)\n+calJac3.2.1.60.genome : Callithrix_jacchus\n+calJac3.2.1.61.genome : Callithrix_jacchus\n+\n+# Canis familiaris genes (CanFam_2.0) (ENSEMBL)\n+canFam2.59.genome : Canis_familiaris\n+canFam2.60.genome : Canis_familiaris\n+canFam2.61.genome : Canis_familiaris\n+\n+# Felis catus genes (CAT) (ENSEMBL)\n+cat1.60.genome : Felis_catus\n+cat1.61.genome : Felis_catus\n+\n+# Cavia porcellus genes (cavPor3) (ENSEMBL)\n+cavPor3.60.genome : Cavia_porcellus\n+cavPor3.61.genome : Cavia_porcellus\n+\n+# Caenorhabditis elegans genes (WS210) (ENSEMBL)\n+ce.WS201.genome : Caenorhabditis_elegans\n+ce.WS210.60.genome : Caenorha"..b', GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Alternative_Yeast_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Ascidian_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Alternative_Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Blepharisma_Macronuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Chlorophycean_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Trematode_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Scenedesmus_obliquus_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+codon.Thraustochytrium_Mitochondrial: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G\n+\n' |
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| diff -r 8d0de9212f4f -r c052639fa666 snpEff_2_1a/snpEff_2_1a/snpEff.jar |
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| Binary file snpEff_2_1a/snpEff_2_1a/snpEff.jar has changed |