miga-base 0.7.26.3 → 1.0.0.sr1
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- checksums.yaml +4 -4
- data/lib/miga/_data/aai-intax.blast.tsv.gz +0 -0
- data/lib/miga/_data/aai-intax.diamond.tsv.gz +0 -0
- data/lib/miga/_data/aai-novel.blast.tsv.gz +0 -0
- data/lib/miga/_data/aai-novel.diamond.tsv.gz +0 -0
- data/lib/miga/cli/action/doctor.rb +50 -19
- data/lib/miga/cli/action/doctor/base.rb +20 -18
- data/lib/miga/cli/action/init.rb +11 -7
- data/lib/miga/cli/action/init/files_helper.rb +1 -0
- data/lib/miga/cli/action/ncbi_get.rb +3 -3
- data/lib/miga/cli/action/tax_dist.rb +2 -2
- data/lib/miga/cli/action/wf.rb +5 -4
- data/lib/miga/daemon.rb +11 -4
- data/lib/miga/dataset/result.rb +10 -6
- data/lib/miga/json.rb +1 -2
- data/lib/miga/metadata.rb +5 -1
- data/lib/miga/parallel.rb +11 -6
- data/lib/miga/project.rb +8 -8
- data/lib/miga/project/base.rb +4 -4
- data/lib/miga/project/result.rb +2 -2
- data/lib/miga/sqlite.rb +7 -0
- data/lib/miga/version.rb +23 -9
- data/scripts/aai_distances.bash +16 -18
- data/scripts/ani_distances.bash +16 -17
- data/scripts/assembly.bash +31 -16
- data/scripts/haai_distances.bash +3 -27
- data/scripts/miga.bash +6 -4
- data/scripts/p.bash +1 -1
- data/scripts/read_quality.bash +9 -18
- data/scripts/trimmed_fasta.bash +14 -30
- data/scripts/trimmed_reads.bash +36 -36
- data/test/parallel_test.rb +31 -0
- data/test/project_test.rb +2 -1
- data/utils/distance/commands.rb +1 -0
- data/utils/distance/runner.rb +2 -4
- data/utils/enveomics/Manifest/Tasks/fasta.json +39 -3
- data/utils/enveomics/Manifest/Tasks/fastq.json +50 -2
- data/utils/enveomics/Manifest/Tasks/mapping.json +70 -0
- data/utils/enveomics/Manifest/Tasks/other.json +77 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +138 -1
- data/utils/enveomics/Manifest/categories.json +13 -4
- data/utils/enveomics/Scripts/Aln.cat.rb +206 -148
- data/utils/enveomics/Scripts/FastA.N50.pl +33 -29
- data/utils/enveomics/Scripts/FastA.fragment.rb +69 -61
- data/utils/enveomics/Scripts/FastA.sample.rb +61 -46
- data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
- data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +59 -52
- data/utils/enveomics/Scripts/SRA.download.bash +6 -8
- data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
- data/utils/enveomics/Scripts/aai.rb +3 -2
- data/utils/enveomics/Scripts/anir.rb +137 -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 +17 -17
- 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/match.rb +63 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -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/utils.rb +73 -0
- data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
- data/utils/enveomics/Scripts/rbm.rb +87 -133
- data/utils/enveomics/Scripts/sam.filter.rb +148 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +2 -2
- data/utils/enveomics/enveomics.R/NAMESPACE +1 -1
- data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
- data/utils/enveomics/enveomics.R/R/utils.R +30 -0
- data/utils/enveomics/enveomics.R/README.md +1 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +10 -2
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +16 -4
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +13 -3
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +9 -2
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +13 -5
- data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +9 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +23 -6
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +13 -4
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +7 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +14 -3
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +10 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +17 -9
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +6 -2
- data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +14 -5
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +19 -4
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +11 -3
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +11 -4
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +26 -12
- 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
- data/utils/requirements.txt +4 -3
- metadata +33 -6
- data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +0 -30
data/utils/requirements.txt
CHANGED
@@ -13,9 +13,10 @@ Prodigal prodigal http://prodigal.ornl.gov
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13
13
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MCL mcl http://micans.org/mcl/
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14
14
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Barrnap barrnap http://www.vicbioinformatics.com/software.barrnap.shtml
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15
15
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IDBA (reads) idba_ud http://i.cs.hku.hk/~alse/hkubrg/projects/idba
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16
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-
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17
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-
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18
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-
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16
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+
FaQCs (reads) FaQCs https://github.com/LANL-Bioinformatics/FaQCs
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17
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+
Falco (reads) falco https://github.com/smithlabcode/falco
|
18
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+
Seqtk (reads) seqtk https://github.com/lh3/seqtk
|
19
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+
Fastp (reads) fastp https://github.com/OpenGene/fastp
|
19
20
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OpenJDK (rdp) java https://adoptopenjdk.net/ Any Java VM would work
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20
21
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MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
|
21
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Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: miga-base
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3
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version: !ruby/object:Gem::Version
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-
version: 0.
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4
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+
version: 1.0.0.sr1
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5
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platform: ruby
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6
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authors:
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- Luis M. Rodriguez-R
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8
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autorequire:
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9
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bindir: bin
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cert_chain: []
|
11
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-
date: 2021-
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11
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+
date: 2021-04-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: daemons
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@@ -110,8 +110,12 @@ files:
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- lib/miga.rb
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- lib/miga/_data/aai-intax-blast.tsv.gz
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- lib/miga/_data/aai-intax-diamond.tsv.gz
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- lib/miga/_data/aai-intax.blast.tsv.gz
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- lib/miga/_data/aai-intax.diamond.tsv.gz
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- lib/miga/_data/aai-novel-blast.tsv.gz
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- lib/miga/_data/aai-novel-diamond.tsv.gz
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- lib/miga/_data/aai-novel.blast.tsv.gz
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- lib/miga/_data/aai-novel.diamond.tsv.gz
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- lib/miga/cli.rb
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- lib/miga/cli/action.rb
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- lib/miga/cli/action/about.rb
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@@ -241,6 +245,7 @@ files:
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- test/lair_test.rb
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- test/metadata_test.rb
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- test/net_test.rb
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+
- test/parallel_test.rb
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- test/project_test.rb
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- test/remote_dataset_test.rb
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- test/result_stats_test.rb
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@@ -375,9 +380,11 @@ files:
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- utils/enveomics/Scripts/FastA.split.rb
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- utils/enveomics/Scripts/FastA.subsample.pl
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- utils/enveomics/Scripts/FastA.tag.rb
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+
- utils/enveomics/Scripts/FastA.toFastQ.rb
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- utils/enveomics/Scripts/FastA.wrap.rb
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- utils/enveomics/Scripts/FastQ.filter.pl
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- utils/enveomics/Scripts/FastQ.interpose.pl
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- utils/enveomics/Scripts/FastQ.maskQual.rb
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- utils/enveomics/Scripts/FastQ.offset.pl
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- utils/enveomics/Scripts/FastQ.split.pl
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- utils/enveomics/Scripts/FastQ.tag.rb
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@@ -406,6 +413,7 @@ files:
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- utils/enveomics/Scripts/Table.df2dist.R
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- utils/enveomics/Scripts/Table.filter.pl
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- utils/enveomics/Scripts/Table.merge.pl
|
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+
- utils/enveomics/Scripts/Table.prefScore.R
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- utils/enveomics/Scripts/Table.replace.rb
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- utils/enveomics/Scripts/Table.round.rb
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- utils/enveomics/Scripts/Table.split.pl
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@@ -414,18 +422,28 @@ files:
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- utils/enveomics/Scripts/VCF.SNPs.rb
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- utils/enveomics/Scripts/aai.rb
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- utils/enveomics/Scripts/ani.rb
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+
- utils/enveomics/Scripts/anir.rb
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- utils/enveomics/Scripts/clust.rand.rb
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- utils/enveomics/Scripts/gi2tax.rb
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- utils/enveomics/Scripts/in_silico_GA_GI.pl
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- utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
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- utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz
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- utils/enveomics/Scripts/lib/enveomics.R
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+
- utils/enveomics/Scripts/lib/enveomics_rb/anir.rb
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+
- utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
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+
- utils/enveomics/Scripts/lib/enveomics_rb/errors.rb
|
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+
- utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
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+
- utils/enveomics/Scripts/lib/enveomics_rb/match.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/og.rb
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+
- utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
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-
- utils/enveomics/Scripts/lib/enveomics_rb/
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+
- utils/enveomics/Scripts/lib/enveomics_rb/stats.rb
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+
- utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/utils.rb
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- utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
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- utils/enveomics/Scripts/ogs.annotate.rb
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- utils/enveomics/Scripts/ogs.core-pan.rb
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@@ -433,7 +451,9 @@ files:
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- utils/enveomics/Scripts/ogs.mcl.rb
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- utils/enveomics/Scripts/ogs.rb
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- utils/enveomics/Scripts/ogs.stats.rb
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- utils/enveomics/Scripts/rbm-legacy.rb
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- utils/enveomics/Scripts/rbm.rb
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- utils/enveomics/Scripts/sam.filter.rb
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- utils/enveomics/Tests/Makefile
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- utils/enveomics/Tests/Mgen_M2288.faa
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- utils/enveomics/Tests/Mgen_M2288.fna
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@@ -471,6 +491,7 @@ files:
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- utils/enveomics/enveomics.R/R/cliopts.R
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- utils/enveomics/enveomics.R/R/df2dist.R
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- utils/enveomics/enveomics.R/R/growthcurve.R
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- utils/enveomics/enveomics.R/R/prefscore.R
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- utils/enveomics/enveomics.R/R/recplot.R
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- utils/enveomics/enveomics.R/R/recplot2.R
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- utils/enveomics/enveomics.R/R/tribs.R
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@@ -496,6 +517,7 @@ files:
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- utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
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- utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
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- utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
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- utils/enveomics/enveomics.R/man/enve.prefscore.Rd
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- utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
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- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
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- utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
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- utils/enveomics/enveomics.R/man/enve.selvector.Rd
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- utils/enveomics/enveomics.R/man/enve.tribs.Rd
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- utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
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@@ -537,6 +560,10 @@ files:
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- utils/enveomics/manifest.json
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- utils/find-medoid.R
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- utils/index_metadata.rb
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- utils/multitrim/Multitrim How-To.pdf
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- utils/multitrim/README.md
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- utils/multitrim/multitrim.py
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- utils/multitrim/multitrim.yml
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- utils/mytaxa_scan.R
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@@ -572,11 +599,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '2.3'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">"
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- !ruby/object:Gem::Version
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version:
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version: 1.3.1
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requirements: []
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rubygems_version: 3.1.
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rubygems_version: 3.1.6
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signing_key:
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specification_version: 4
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summary: MiGA
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@@ -1,30 +0,0 @@
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1
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-
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module Enve
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class Stat
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# Generates a random number from the +dist+ distribution with +params+
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# parameters. This is simply a wrapper to the r_* functions below.
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def self.rand(dist=:unif, *params)
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send("r_#{dist}", *params)
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end
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# Generates a random number from the uniform distribution between +min+ and
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# +max+. By default generates random numbers between 0.0 and 1.0.
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def self.r_unif(min=0.0, max=1.0)
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min + (max-min)*Random::rand
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end
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# Generates a random number from the geometric distribution with support
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# {0, 1, 2, ...} and probability of success +p+.
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-
def self.r_geom(p)
|
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(Math::log(1.0 - rand)/Math::log(1.0-p) - 1.0).ceil
|
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-
end
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# Generates a random number from the shifted geometric distribution with
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# support {1, 2, 3, ...} and probability of success +p+.
|
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def self.r_sgeom(p)
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(Math::log(1.0 - rand)/Math::log(1.0-p)).ceil
|
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end
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end
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end
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