miga-base 1.2.17.0 → 1.2.17.1
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- checksums.yaml +4 -4
- data/lib/miga/version.rb +1 -1
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
- data/utils/FastAAI/FastAAI +3659 -0
- data/utils/FastAAI/FastAAI-legacy/FastAAI +1336 -0
- data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +1296 -0
- data/utils/FastAAI/README.md +84 -0
- data/utils/enveomics/Docs/recplot2.md +244 -0
- data/utils/enveomics/Examples/aai-matrix.bash +66 -0
- data/utils/enveomics/Examples/ani-matrix.bash +66 -0
- data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
- data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
- data/utils/enveomics/LICENSE.txt +73 -0
- data/utils/enveomics/Makefile +52 -0
- data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
- data/utils/enveomics/Manifest/Tasks/blasttab.json +790 -0
- data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
- data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
- data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
- data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
- data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
- data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
- data/utils/enveomics/Manifest/Tasks/other.json +906 -0
- data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +650 -0
- data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
- data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
- data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
- data/utils/enveomics/Manifest/categories.json +165 -0
- data/utils/enveomics/Manifest/examples.json +162 -0
- data/utils/enveomics/Manifest/tasks.json +4 -0
- data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
- data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
- data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
- data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
- data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
- data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
- data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
- data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
- data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
- data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
- data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
- data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
- data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
- data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
- data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
- data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
- data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
- data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
- data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
- data/utils/enveomics/README.md +42 -0
- data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
- data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
- data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
- data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
- data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
- data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
- data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
- data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
- data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
- data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
- data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
- data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
- data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
- data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
- data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
- data/utils/enveomics/Scripts/Chao1.pl +97 -0
- data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
- data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
- data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
- data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
- data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
- data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
- data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
- data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
- data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
- data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
- data/utils/enveomics/Scripts/FastA.length.pl +38 -0
- data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
- data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
- data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
- data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
- data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
- data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
- data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
- data/utils/enveomics/Scripts/FastA.split.pl +55 -0
- data/utils/enveomics/Scripts/FastA.split.rb +79 -0
- data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
- data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
- data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
- data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
- data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
- data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
- data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
- data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
- data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
- data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
- data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
- data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
- data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
- data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
- data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
- data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
- data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
- data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
- data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
- data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
- data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
- data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
- data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
- data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
- data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
- data/utils/enveomics/Scripts/SRA.download.bash +55 -0
- data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
- data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
- data/utils/enveomics/Scripts/Table.barplot.R +31 -0
- data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
- data/utils/enveomics/Scripts/Table.filter.pl +61 -0
- data/utils/enveomics/Scripts/Table.merge.pl +77 -0
- data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
- data/utils/enveomics/Scripts/Table.replace.rb +69 -0
- data/utils/enveomics/Scripts/Table.round.rb +63 -0
- data/utils/enveomics/Scripts/Table.split.pl +57 -0
- data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
- data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
- data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
- data/utils/enveomics/Scripts/aai.rb +421 -0
- data/utils/enveomics/Scripts/ani.rb +362 -0
- data/utils/enveomics/Scripts/anir.rb +137 -0
- data/utils/enveomics/Scripts/clust.rand.rb +102 -0
- data/utils/enveomics/Scripts/gi2tax.rb +103 -0
- data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
- data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
- data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
- data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
- data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
- data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
- data/utils/enveomics/Scripts/ogs.rb +104 -0
- data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
- data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
- data/utils/enveomics/Scripts/rbm.rb +108 -0
- data/utils/enveomics/Scripts/sam.filter.rb +148 -0
- data/utils/enveomics/Tests/Makefile +10 -0
- data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
- data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
- data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
- data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
- data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
- data/utils/enveomics/Tests/alkB.nwk +1 -0
- data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
- data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
- data/utils/enveomics/Tests/hiv1.faa +59 -0
- data/utils/enveomics/Tests/hiv1.fna +134 -0
- data/utils/enveomics/Tests/hiv2.faa +70 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
- data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
- data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
- data/utils/enveomics/build_enveomics_r.bash +45 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
- data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
- data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
- data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
- data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
- data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
- data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
- data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
- data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
- data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
- data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
- data/utils/enveomics/enveomics.R/R/utils.R +80 -0
- data/utils/enveomics/enveomics.R/README.md +81 -0
- data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
- data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
- data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
- data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
- data/utils/enveomics/globals.mk +8 -0
- data/utils/enveomics/manifest.json +9 -0
- data/utils/multitrim/Multitrim How-To.pdf +0 -0
- data/utils/multitrim/README.md +67 -0
- data/utils/multitrim/multitrim.py +1555 -0
- data/utils/multitrim/multitrim.yml +13 -0
- metadata +301 -5
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#!/usr/bin/env perl
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# @author Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
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# @update Mar-23-2015
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# @license Artistic License 2.0
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use warnings;
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use strict;
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use List::Util qw/sum max/;
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use Getopt::Std;
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use Math::Round qw/round/;
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our $VERSION = 1.1;
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warn <<WARN
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┌──[ IMPORTANT ]─────────────────────────────────────────────────┐
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│ This script has been deprecated in favor of JPlace.to_iToL.rb. │
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│ Please use the new version, together with the RAxML EPA's file │
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│ RAxML_portableTree.*.jplace instead. │
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└────────────────────────────────────────────────────────────────┘
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WARN
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;
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sub HELP_MESSAGE {
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die "
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Description:
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Reformats the node names (labels) of a RAxML_originalLabelledTree.<NAME> file
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(produced by RAxML's EPA, -f v), so it can be opened in most tree viewers (like
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iToL and FigTree). Also, it creates iToL-compatible files to draw pie-charts
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(based on the classification of short reads) in the nodes of the reference tree.
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Usage:
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$0 -n <NAME> [other options...]
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-n <str> * Name of the run used in RAxML.
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-t <str> Use this file as original labelled tree, instead of generating one
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based on the job name. By default, RAxML_originalLabelledTree.<NAME>
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in the -d directory. See [NOTE1].
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-d <str> Directory containing RAxML files. By default: current directory.
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-o <str> Output tree. By default, it takes the path to the input tree and
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appends .nwk to it.
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-l <str> File containing a list of internal nodes. The nodes in the list
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will be renamed, and the reads of all children nodes will be
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transferred to it. This can be useful if you want to display
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these nodes collapsed. The format of the file is raw text, with
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two columns separated by tabs or spaces, where the first column is
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the original name of the internal node (without the brackets) and
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the second is the name to be used. See [NOTE2].
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-a Append original label to the renamed nodes (only if -l is passed).
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-s <str> The names of the reads will be assumed to contain the sample name,
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separated by this string. For example, if the value is '_', and
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a read has the name 'hco_ABCDEF/1#ACTG', it will be assumed to be
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a read from the sample 'hco'. If not provided, all the reads are
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assumed to come from the same sample (called 'unknown').
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-m <str> Comma-delimited list of samples. If not provided, all found samples
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will be used (unsorted).
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-c <str> Comma-delimited list of colors (in RGB hexadecimal) to represent
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the different samples. If not provided (or if insufficient values
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are provided) random colors are generated.
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-N <str> Comma-delimited list of normalizing factors per dataset. Typically,
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the size of the datasets divided by a fixed value (e.g. size x 1,000,
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to express sizes as reads per thousand).
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-T Use the total number of assigned reads per sample (times a constant)
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as the normalizing factor. The constant used corresponds to the 100
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times the size of the largest factor. If passed, -N is ignored.
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-q Run quietly.
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-h/--help Displays this message and exits.
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* Mandatory
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[NOTE1] The tree provided by -t MUST be based on a tree produced by this script
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without the -l option.
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[NOTE2] The tree produced by RAxML-EPA is usually not correctly rooted, which
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makes the -l option useless. However, you can manually root the tree and provide
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the rooted tree in Newick format using the -t option. If you do this, make
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sure the program doesn't change/delete the names of the internal nodes. I know
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that iToL can do it correctly (if you export preserving the original IDs), while
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FigTree deletes the labels. I didn't try any other tool.
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";
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}
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my %o;
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getopts('n:t:d:o:l:s:m:c:N:Tqh', \%o);
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$o{d} ||= '.';
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$o{n} or &HELP_MESSAGE;
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$o{h} and &HELP_MESSAGE;
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$o{c} = [split /,/, (defined $o{c}?$o{c}:"")];
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$o{N} = [split /,/, (defined $o{N}?$o{N}:"")];
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# Set files
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my $inTree = ($o{t} || $o{d}."/RAxML_originalLabelledTree.".$o{n});
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my $outTree = ($o{o} || $inTree.".nwk");
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my $inClass = $o{d}."/RAxML_classification.".$o{n};
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my $outClass = $inClass.".iToL";
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my $outColl = $outTree.".collapse.iToL";
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# Relocate tree node names
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print STDERR "o Reformatting tree.\n" unless $o{q};
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open INTREE, "<", $inTree or die "Cannot read file: $inTree: $!\n";
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my $tree = <INTREE>;
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$tree =~ s/:([\d\.]+)(\[.+?\])/$2:$1/g unless $o{t};
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close INTREE;
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# Read leaf nodes
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print STDERR "o Reading nodes.\n" unless $o{q};
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my %tags = ();
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my $t = $tree;
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while($t =~ m/([A-Za-z0-9_\|\.-]+\[([A-Za-z0-9_\|\.-]+)\])/){
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my $n = $1;
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my $ta = $2;
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$tags{$ta} = $n;
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$t = substr $t, (length($n) + index $t, $n);
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}
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# Label/collapse internal nodes
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if($o{l}){
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print STDERR "o Labeling/collapsing internal nodes.\n";
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open LIST, "<", $o{l} or die "Cannot read file: $o{l}: $!\n";
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open COLL, ">", $outColl or die "Cannot create file: $outColl: $!\n";
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while(<LIST>){
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chomp;
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next if /^#/ or /^\s*$/;
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# Label internal node
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my @l = split /\s+/;
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$l[0] =~ m/^\[(.+)\]$/ or die "Unable to parse internal node name: $l[0].\n";
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my $ori = $1;
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my $new = $l[1];
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if(exists $tags{$ori}){
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warn "Warning: Trying to label/collapse $ori as $new, already defined as $tags{$ori}.\n";
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next;
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}
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$new =~ s/[^A-Za-z0-9_\|\.\-]/_/g;
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$new.= "[$ori]" if $o{a};
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$tags{$ori} = $new;
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$tree =~ s/\[$ori\]/$new/;
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# Isolate node
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$t = substr $tree, 0, index($tree, $new);
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my $i=length($t)-2;
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for(my $c=1 ; $i and $c; $i--){
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my $char = substr $t, $i, 1;
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$c++ if $char eq ')';
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$c-- if $char eq '(';
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}
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$t = substr $t, $i;
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# Get children
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$t =~ s/:[\d\.]+|[\(\)]/,/g;
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$t =~ s/,+/,/g;
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my $chn=0;
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for my $child (split /,/, $t){
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next unless $child;
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$child =~ s/.*\[(.+?)\]/$1/;
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$tags{$child} = $new;
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$chn++;
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}
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print STDERR " Collapsing $new: $chn children.\n" unless $o{q};
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print COLL "$new\n";
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}
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close LIST;
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close COLL;
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}
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# Save tree
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open OUTTREE, ">", $outTree or die "Cannot create file: $outTree: $!\n";
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print OUTTREE $tree;
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close OUTTREE;
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# Count reads
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my %samples = ();
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my %nodes = ();
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print STDERR "o Counting reads.\n";
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my $s = defined $o{s} ? $o{s} : "";
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open INCLASS, "<", $inClass or die "Cannot read file: $inClass: $!\n";
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while(<INCLASS>){
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my @ln = split /\s+/;
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$ln[0] =~ s/$s.+$//; # Sample name
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($samples{$ln[0]} ||= 0)++;
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$tags{$ln[1]} ||= "[".$ln[1]."]"; # Node name
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(($nodes{$tags{$ln[1]}} ||= {})->{$ln[0]} ||= 0)++;
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}
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close INCLASS;
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my $labs = 'LABELS';
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my $cols = 'COLORS';
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my @samples = $o{m} ? (split /,/, $o{m}) : (keys %samples);
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my @normfac = ();
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for my $sample (@samples){
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my $col = shift @{$o{c}};
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unless(defined $col and length($col)==6){
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$col = '';
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for (1 .. 3){
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my $v = int rand 16;
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$v = chr $v+55 if $v>9;
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$col.="$v$v";
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}
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}
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my $nf = shift @{$o{N}};
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$nf = 1 unless defined $nf and $nf>0;
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$labs.= ','.($sample || 'unknown');
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$cols.= ',#'.$col;
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push @normfac, $nf+0;
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}
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open OUTCLASS, ">", $outClass or die "Cannot create file: $outClass: $!\n";
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print OUTCLASS "$labs\n$cols\n";
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my $tiny=0;
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for my $node (keys %nodes){
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my $i=0;
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for my $s (@samples){
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$nodes{$node}->{$s} = ($nodes{$node}->{$s} || 0)/($o{T} ? ($samples{$s}||1)/(max(values %samples)*100) : ($normfac[$i++]||1));
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}
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my $r = round(sum(values %{$nodes{$node}}));
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print OUTCLASS "$node,R$r";
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for my $sample (@samples){
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print OUTCLASS ",".round($nodes{$node}->{$sample} || 0);
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}
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print OUTCLASS "\n";
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$tiny++ unless $r;
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}
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close OUTCLASS;
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unless($o{q}) {
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print "Total counts per dataset:\n";
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print " $_\t".($samples{$_}||0)."\n" for @samples;
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}
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warn "$tiny node assignments are too small to represent. Decrease the values of -N or use an alternative like -T." if $tiny;
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#!/usr/bin/env Rscript
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#
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# @author Luis M. Rodriguez-R
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# @update Jan-04-2016
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# @license artistic license 2.0
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#
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#= Load stuff
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args <- commandArgs(trailingOnly = F)
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enveomics_R <- file.path(dirname(
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sub("^--file=", "", args[grep("^--file=", args)])),
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"lib", "enveomics.R")
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library(methods)
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source(file.path(enveomics_R, "R", "cliopts.R"))
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source(file.path(enveomics_R, "R", "recplot2.R"))
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#= Generate interface
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opt <- enve.cliopts(enve.recplot2.compareIdentities,
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file.path(enveomics_R, "man", "enve.recplot2.compareIdentities.Rd"),
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positional_arguments=2,
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usage="usage: %prog [options] recplot-A.Rdata recplot-B.Rdata",
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number=c("pseudocounts", "max.deviation"), ignore=c("x", "y"),
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p_desc="Calculates the difference between identity distributions of two recruitment plots.")
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#= Run it!
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load(opt$args[1])
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opt$options[['x']] <- rp
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load(opt$args[2])
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opt$options[['y']] <- rp
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dist <- do.call("enve.recplot2.compareIdentities", opt$options)
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cat(dist, '\n')
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#!/bin/bash
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#
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# @author Luis M. Rodriguez-R
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# @update Oct-20-2015
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# @license artistic license 2.0
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#
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FTP="ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria"
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ORG=$1
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EXT=${2:-.*.gz}
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STT=${3:-Any}
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DIR=${4:-$ORG}
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if [[ "$ORG" == "" ]] ; then
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echo "
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Downloads a collection of sequences and/or annotations from NCBI's RefSeq.
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Usage:
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$0 <organism> [<extension>[ <level>[ <dir>]]]
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<organism> The organism to download (e.g., Streptococcus_pneumoniae).
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<extension> Extension to download. Common extensions include '.fna.gz'
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(genomic sequences), '.faa.gz' (protein sequences), and
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'.gff.gz' (annotations). By default: '.*.gz' (all data).
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<level> Use only genomes with this assembly level. Common levels are
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'Complete Genome' and 'Contig'. By default, any assembly
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level is allowed ('Any').
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<dir> Directory where the files are to be downladed. By default,
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same as <organism>.
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" >&2
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exit
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fi
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[[ -d "$DIR" ]] || mkdir "$DIR"
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curl -s "$FTP/$ORG/assembly_summary.txt" -o "$DIR/assembly_summary.txt"
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for path in $(cat "$DIR/assembly_summary.txt" \
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| awk -F"\t" "\$12==\"$STT\" || \"$STT\"==\"Any\" {print \$20}" ) ; do
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dir="$DIR/$(basename "$path")"
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[[ -d "$dir" ]] || mkdir "$dir"
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for file in $(curl -s "$path/" | awk '{print $9}') ; do
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if [[ "$file" == *$EXT ]] ; then
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curl -s "$path/$file" -o "$dir/$file"
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fi
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done
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done
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@@ -0,0 +1,55 @@
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#!/bin/bash
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DATA_LINK="https://www.ebi.ac.uk/ena/portal/api/filereport"
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DATA_OPS="result=read_run&fields=run_accession,fastq_ftp,fastq_md5"
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SRX=$1
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DIR=${2:-$SRX}
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VERSION=1.0
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if [[ "$SRX" == "" ]] ; then
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echo "
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[Enveomics Collection: $(basename "$0" .bash) $VERSION]
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Downloads the set of runs from a project, sample, or experiment in SRA.
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Usage:
|
16
|
+
$(basename "$0") <SRA-ID>[ <dir>]
|
17
|
+
|
18
|
+
<SRA-ID> ID of the SRA Project, Sample, or Experiment.
|
19
|
+
<dir> Directory where the files are to be downladed. By default,
|
20
|
+
same as <SRA-ID>.
|
21
|
+
" >&2
|
22
|
+
exit
|
23
|
+
fi
|
24
|
+
|
25
|
+
[[ -d "$DIR" ]] || mkdir "$DIR"
|
26
|
+
|
27
|
+
function md5value {
|
28
|
+
local file=$1
|
29
|
+
o=$(md5 "$file" | perl -pe 's/.* //')
|
30
|
+
[[ -n $o ]] || o=$(md5sum-lite "$file" | awk '{print $1}')
|
31
|
+
[[ -n $o ]] || o=$(md5sum "$file" | awk '{print $1}')
|
32
|
+
echo "$o"
|
33
|
+
}
|
34
|
+
|
35
|
+
curl -Ls "$DATA_LINK?$DATA_OPS&accession=$SRX" -o "$DIR/srr_list.txt"
|
36
|
+
tail -n +2 "$DIR/srr_list.txt" | while read ln ; do
|
37
|
+
srr=$(echo "$ln"|cut -f 1)
|
38
|
+
ftp=$(echo "$ln"|cut -f 2)
|
39
|
+
md5=$(echo "$ln"|cut -f 3)
|
40
|
+
dir="$DIR/$srr"
|
41
|
+
[[ -d "$dir" ]] || mkdir "$dir"
|
42
|
+
echo "o $srr" >&2
|
43
|
+
for uri in $(echo "$ftp" | tr ";" " ") ; do
|
44
|
+
file="$dir/$(basename $uri)"
|
45
|
+
curl "$uri" -o "$file"
|
46
|
+
md5obs=$(md5value "$file" 2> /dev/null)
|
47
|
+
if [[ "$md5" == "$md5obs"* ]] ; then
|
48
|
+
md5=$(echo "$md5" | perl -pe 's/^[^;]+;//')
|
49
|
+
else
|
50
|
+
echo "Corrupt file: $file" >&2
|
51
|
+
echo " MD5 mismatch: $md5obs not in $md5" >&2
|
52
|
+
exit 1;
|
53
|
+
fi
|
54
|
+
done
|
55
|
+
done
|
@@ -0,0 +1,36 @@
|
|
1
|
+
#!/usr/bin/env Rscript
|
2
|
+
#
|
3
|
+
# @author Luis M. Rodriguez-R
|
4
|
+
# @update Jan-05-2016
|
5
|
+
# @license artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
#= Load stuff
|
9
|
+
suppressPackageStartupMessages(library(enveomics.R))
|
10
|
+
args <- commandArgs(trailingOnly = F)
|
11
|
+
enveomics_R <- file.path(dirname(
|
12
|
+
sub("^--file=", "", args[grep("^--file=", args)])),
|
13
|
+
"lib", "enveomics.R")
|
14
|
+
|
15
|
+
#= Generate interface
|
16
|
+
opt <- enve.cliopts(plot.enve.TRIBStest,
|
17
|
+
file.path(enveomics_R, "man", "plot.enve.TRIBStest.Rd"),
|
18
|
+
positional_arguments=c(1,3),
|
19
|
+
usage="usage: %prog [options] output.pdf [width height]",
|
20
|
+
mandatory=c("x"),
|
21
|
+
vectorize=c("xlim","ylim"),
|
22
|
+
number=c("xlim","ylim"),
|
23
|
+
defaults=c(type="overlap", xlim=NA, ylim=NA))
|
24
|
+
|
25
|
+
#= Run it!
|
26
|
+
a <- new.env()
|
27
|
+
load(opt$options[['x']], a)
|
28
|
+
opt$options[['x']] <- get(ls(envir=a),envir=a)
|
29
|
+
summary(opt$options[['x']])
|
30
|
+
if(is.na(opt$options[['xlim']][1])) opt$options[['xlim']] <- NULL
|
31
|
+
if(is.na(opt$options[['ylim']][1])) opt$options[['ylim']] <- NULL
|
32
|
+
args = as.list(opt$args)
|
33
|
+
for(i in 2:3) if(length(args)>=i) args[[i]] <- as.numeric(args[[i]])
|
34
|
+
do.call("pdf", args)
|
35
|
+
do.call("plot.enve.TRIBStest", opt$options)
|
36
|
+
dev.off()
|
@@ -0,0 +1,39 @@
|
|
1
|
+
#!/usr/bin/env Rscript
|
2
|
+
#
|
3
|
+
# @author Luis M. Rodriguez-R
|
4
|
+
# @update Jan-05-2016
|
5
|
+
# @license artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
#= Load stuff
|
9
|
+
suppressPackageStartupMessages(library(enveomics.R))
|
10
|
+
args <- commandArgs(trailingOnly = F)
|
11
|
+
enveomics_R <- file.path(dirname(
|
12
|
+
sub("^--file=", "", args[grep("^--file=", args)])),
|
13
|
+
"lib", "enveomics.R")
|
14
|
+
|
15
|
+
#= Generate interface
|
16
|
+
opt <- suppressWarnings(enve.cliopts(enve.tribs,
|
17
|
+
file.path(enveomics_R, "man", "enve.tribs.Rd"),
|
18
|
+
positional_arguments=c(0,2),
|
19
|
+
usage="usage: %prog [options] [output.Rdata [bins=50]]",
|
20
|
+
mandatory=c("dist", "selection"),
|
21
|
+
defaults=c(dimensions=0, selection=NULL),
|
22
|
+
ignore=c("metaMDS.opts","points","pre.tribs","subsamples"),
|
23
|
+
o_desc=list(dist="A tab-delimited matrix of distances.",
|
24
|
+
selection="A list of names with the selection to evaluate."),
|
25
|
+
p_desc=paste("",
|
26
|
+
"Estimates the empirical difference between all the distances",
|
27
|
+
"in a set of objects and a subset, together with its statistical",
|
28
|
+
"significance.",sep="\n\t")))
|
29
|
+
|
30
|
+
#= Run it!
|
31
|
+
opt$options[['dist']] <- as.dist(read.table(opt$options[['dist']],
|
32
|
+
header=TRUE, sep="\t", row.names=1))
|
33
|
+
opt$options[['selection']] <- read.table(opt$options[['selection']],
|
34
|
+
header=FALSE, sep="\t", as.is=TRUE)[,1]
|
35
|
+
if(opt$options[['dimensions']]==0) opt$options[['dimensions']] <- NULL
|
36
|
+
if(length(opt$args)>1) opt$options[['bins']] <- as.numeric(opt$args[2])
|
37
|
+
t <- do.call("enve.tribs.test", opt$options)
|
38
|
+
summary(t)
|
39
|
+
if(length(opt$args)>0) save(t, file=opt$args[1])
|
@@ -0,0 +1,31 @@
|
|
1
|
+
#!/usr/bin/env Rscript
|
2
|
+
#
|
3
|
+
# @author Luis M. Rodriguez-R
|
4
|
+
# @update Dec-29-2015
|
5
|
+
# @license artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
#= Load stuff
|
9
|
+
args <- commandArgs(trailingOnly = F)
|
10
|
+
enveomics_R <- file.path(dirname(
|
11
|
+
sub("^--file=", "", args[grep("^--file=", args)])),
|
12
|
+
"lib", "enveomics.R")
|
13
|
+
source(file.path(enveomics_R, "R", "cliopts.R"))
|
14
|
+
source(file.path(enveomics_R, "R", "utils.R"))
|
15
|
+
source(file.path(enveomics_R, "R", "barplot.R"))
|
16
|
+
|
17
|
+
#= Generate interface
|
18
|
+
opt <- enve.cliopts(enve.barplot,
|
19
|
+
file.path(enveomics_R, "man", "enve.barplot.Rd"),
|
20
|
+
positional_arguments=c(1,3),
|
21
|
+
usage="usage: %prog [options] output.pdf [width height]",
|
22
|
+
mandatory=c("x"), vectorize=c("sizes","order","col"),
|
23
|
+
number=c("sizes","order"),
|
24
|
+
o_desc=list(x="A tab-delimited file containing header (first row) and row names (first column)."))
|
25
|
+
|
26
|
+
#= Run it!
|
27
|
+
args = as.list(opt$args)
|
28
|
+
for(i in 2:3) if(length(args)>=i) args[[i]] <- as.numeric(args[[i]])
|
29
|
+
do.call("pdf", args)
|
30
|
+
do.call("enve.barplot", opt$options)
|
31
|
+
dev.off()
|
@@ -0,0 +1,30 @@
|
|
1
|
+
#!/usr/bin/env Rscript
|
2
|
+
#
|
3
|
+
# @author Luis M. Rodriguez-R
|
4
|
+
# @update Jan-04-2016
|
5
|
+
# @license artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
#= Load stuff
|
9
|
+
args <- commandArgs(trailingOnly = F)
|
10
|
+
enveomics_R <- file.path(dirname(
|
11
|
+
sub("^--file=", "", args[grep("^--file=", args)])),
|
12
|
+
"lib", "enveomics.R")
|
13
|
+
source(file.path(enveomics_R, "R", "cliopts.R"))
|
14
|
+
source(file.path(enveomics_R, "R", "df2dist.R"))
|
15
|
+
|
16
|
+
#= Generate interface
|
17
|
+
opt <- enve.cliopts(enve.df2dist,
|
18
|
+
file.path(enveomics_R, "man", "enve.df2dist.Rd"),
|
19
|
+
positional_arguments=1,
|
20
|
+
usage="usage: %prog [options] output.mat",
|
21
|
+
mandatory=c("x"),
|
22
|
+
number=c("default.d", "max.sim"),
|
23
|
+
o_desc=list(x="A tab-delimited table with the distances."),
|
24
|
+
p_desc="Transform a tab-delimited list of distances into a squared matrix.")
|
25
|
+
|
26
|
+
#= Run it!
|
27
|
+
opt$options[['x']] <- read.table(opt$options[['x']],
|
28
|
+
header=TRUE, sep="\t", as.is=TRUE)
|
29
|
+
dist <- do.call("enve.df2dist", opt$options)
|
30
|
+
write.table(as.matrix(dist), opt$args[1], quote=FALSE, sep="\t", col.names=NA)
|
@@ -0,0 +1,61 @@
|
|
1
|
+
#!/usr/bin/env perl
|
2
|
+
#
|
3
|
+
# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
|
4
|
+
# @update: Mar-23-2015
|
5
|
+
# @license: artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
use warnings;
|
9
|
+
use strict;
|
10
|
+
use Getopt::Std;
|
11
|
+
|
12
|
+
my %o;
|
13
|
+
getopts('k:s:ihn', \%o);
|
14
|
+
my($list, $table) = @ARGV;
|
15
|
+
|
16
|
+
($list and $table) or die "
|
17
|
+
.Description:
|
18
|
+
Extracts (and re-orders) a subset of rows from a raw table.
|
19
|
+
|
20
|
+
.Usage: $0 [options] list.txt table.txt > subset.txt
|
21
|
+
|
22
|
+
Options:
|
23
|
+
-k <int> Column of the table to use as key to filter. By default, 1.
|
24
|
+
-s <str> String to use as separation between rows. By default, tabulation.
|
25
|
+
-i If set, reports the inverse of the list (i.e., reports only rows
|
26
|
+
absent in the list). Implies -n.
|
27
|
+
-h Keep first row of the table (header) untouched.
|
28
|
+
-n No re-order. The output has the same order of the table. By
|
29
|
+
default, it prints in the order of the list.
|
30
|
+
|
31
|
+
list.txt List of IDs to extract.
|
32
|
+
table.txt Table file containing the superset.
|
33
|
+
subset.txt Table file to be created.
|
34
|
+
|
35
|
+
";
|
36
|
+
|
37
|
+
$o{k} ||= 1;
|
38
|
+
$o{s} ||= "\t";
|
39
|
+
$o{n}=1 if $o{i};
|
40
|
+
my $HEADER = "";
|
41
|
+
|
42
|
+
my $tbl2 = $o{n} ? $list : $table;
|
43
|
+
open TBL, "<", $tbl2 or die "Cannot read file: $tbl2: $!\n";
|
44
|
+
$HEADER = <TBL> if $o{h} and not $o{n};
|
45
|
+
my %tbl2 = map { my $l=$_; chomp $l; my @r=split $o{s}, $l; $r[ $o{n} ? 0 : $o{k}-1] => $l } <TBL>;
|
46
|
+
close TBL;
|
47
|
+
|
48
|
+
my $tbl1 = $o{n} ? $table : $list;
|
49
|
+
open TBL, "<", $tbl1 or die "Cannot read file: $tbl1: $!\n";
|
50
|
+
$HEADER = <TBL> if $o{h} and $o{n};
|
51
|
+
print $HEADER;
|
52
|
+
while(my $ln = <TBL>){
|
53
|
+
chomp $ln;
|
54
|
+
next unless $ln;
|
55
|
+
my @ln = split $o{s}, $ln;
|
56
|
+
my $good = exists $tbl2{ $ln[$o{n} ? $o{k}-1 : 0] };
|
57
|
+
$good = not $good if $o{i};
|
58
|
+
print "".($o{n} ? $ln : $tbl2{$ln[0]})."\n" if $good;
|
59
|
+
}
|
60
|
+
close TBL;
|
61
|
+
|
@@ -0,0 +1,77 @@
|
|
1
|
+
#!/usr/bin/env perl
|
2
|
+
#
|
3
|
+
# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
|
4
|
+
# @update: Sep-20-2015
|
5
|
+
# @license: artistic license 2.0
|
6
|
+
#
|
7
|
+
|
8
|
+
use warnings;
|
9
|
+
use strict;
|
10
|
+
use Getopt::Std;
|
11
|
+
|
12
|
+
my %o;
|
13
|
+
getopts('si:o:ne:h:H:r:', \%o);
|
14
|
+
my @files = @ARGV;
|
15
|
+
|
16
|
+
$#files>0 or die "
|
17
|
+
.Description:
|
18
|
+
Merges multiple (two-column) lists into one table.
|
19
|
+
|
20
|
+
.Usage:
|
21
|
+
$0 [options] files... > output.txt
|
22
|
+
|
23
|
+
Options:
|
24
|
+
-s Values are read as Strings. By default, values are read as numbers.
|
25
|
+
-i <str> Input field-delimiter. By default: tabulation (\"\\t\").
|
26
|
+
-o <str> Output field-delimiter. By default: tabulation (\"\\t\").
|
27
|
+
-n No-header. By default, the header is determined by the file names.
|
28
|
+
-e <str> Default string when no value is found. By default, the \"empty\" value
|
29
|
+
is 0 if values are numeric (i.e., unless -s is set) or an empty string
|
30
|
+
otherwise.
|
31
|
+
-h <str> Header of the first column, containing the IDs. By default: \"Tag\".
|
32
|
+
-H <str> Format of filenames capturing the column header in the first capturing
|
33
|
+
parenthesis. Non-capturing paretheses can be defined as (?:...). By
|
34
|
+
default: \"(?:.*/)?([^\\.]+)\", which captures the part of the basename
|
35
|
+
of the file before the first dot (if any).
|
36
|
+
-r <int> Number of leading rows to ignore in the input files. Zero by default.
|
37
|
+
|
38
|
+
";
|
39
|
+
$o{i} ||= "\t";
|
40
|
+
$o{o} ||= "\t";
|
41
|
+
$o{e} ||= ($o{s} ? "" : 0);
|
42
|
+
$o{h} ||= "Tag";
|
43
|
+
$o{H} ||= "(?:.*/)?([^\\.]+)";
|
44
|
+
$o{r} += 0;
|
45
|
+
|
46
|
+
my $notes = {};
|
47
|
+
|
48
|
+
print $o{h} unless $o{n};
|
49
|
+
my $i = 0;
|
50
|
+
for my $file (@files){
|
51
|
+
unless($o{n}){
|
52
|
+
$file =~ m/$o{H}/ or die "Filename '$file' doesn't match format '$o{H}'.";
|
53
|
+
my $tag=$1;
|
54
|
+
print $o{o}.$tag;
|
55
|
+
}
|
56
|
+
open IN, "<", $file or die "Cannot read file: $file: $!\n";
|
57
|
+
while(<IN>){
|
58
|
+
next if $. <= $o{r};
|
59
|
+
chomp;
|
60
|
+
my @l = split $o{i};
|
61
|
+
$l[1]+=0 unless $o{s};
|
62
|
+
$notes->{$l[0]} ||= [];
|
63
|
+
$notes->{$l[0]}->[$i] = $l[1];
|
64
|
+
}
|
65
|
+
close IN;
|
66
|
+
$i++;
|
67
|
+
}
|
68
|
+
print "\n" unless $o{n};
|
69
|
+
|
70
|
+
for my $id (keys %$notes){
|
71
|
+
print $id;
|
72
|
+
for my $i (0 .. $#files){
|
73
|
+
print $o{o}.(( defined $notes->{$id}->[$i] ? $notes->{$id}->[$i] : $o{e} ));
|
74
|
+
}
|
75
|
+
print "\n";
|
76
|
+
}
|
77
|
+
|