miga-base 0.3.9.0 → 0.3.9.1

data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd

@@ -6,23 +6,25 @@ depth.}
 \usage{enve.recplot2.extractWindows(rp, peak, lower.tail = TRUE, significance = 0.05, 
     seq.names = FALSE)}
 \arguments{
-  \item{rp}{Recruitment plot, a enve.RecPlot2 object.}
+  \item{rp}{Recruitment plot, a `enve.RecPlot2` object.}
   \item{peak}{Peak, an `enve.RecPlot2.Peak` object. If list, it is assumed to be a
-list of enve.RecPlot2.Peak objects, in which case the core peak is
+list of `enve.RecPlot2.Peak` objects, in which case the core peak is
 used (see `enve.recplot2.corePeak`).}
   \item{lower.tail}{If FALSE, it returns windows significantly above the peak in
 sequencing depth.}
   \item{significance}{Significance threshold (alpha) to select windows.}
   \item{seq.names}{Returns subject sequence names instead of a vector of Booleans. If
-the recruitment plot was generated with pos.breaks=0 it returns a
-vector of characters (the sequence identifiers), otherwise it returns
-a data.frame with a name column and two columns of coordinates.}
+the recruitment plot was generated with named position bins (e.g, using
+`pos.breaks`=0 or a two-column `pos.breaks.tsv`), it returns a vector of
+characters (the sequence identifiers), otherwise it returns a data.frame
+with a name column and two columns of coordinates.}
 }
 
 \value{Returns a vector of logicals if `seq.names=FALSE`. If `seq.names=TRUE`,
-it returns a vector of characters if the object was built with
-`pos.breaks=0` or a data.frame with four columns otherwise: name.from,
-name.to, pos.from, and pos.to (see `enve.recplot2.coordinates`).}
+it returns a vector of characters if the object has `pos.names` defined,
+or a data.frame with four columns otherwise:
+name.from, name.to, pos.from, and pos.to
+(see `enve.recplot2.coordinates`).}
 
 \author{Luis M. Rodriguez-R [aut, cre]}
 

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd

@@ -17,7 +17,7 @@ sub-population mixtures, using a custom distribution-mowing method.}
 (`quant.est`) to estimate a peak.}
   \item{quant.est}{Range of quantiles to be used in the estimation of a peak's
 parameters.}
-  \item{mlv.opts}{Options passed to `mlv` to estimate the mode.}
+  \item{mlv.opts}{Ignored. For backwards compatibility.}
   \item{fitdist.opts.sn}{
 }
   \item{fitdist.opts.norm}{

data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd

@@ -0,0 +1,26 @@
+\name{enve.recplot2.windowDepthThreshold}
+\alias{enve.recplot2.windowDepthThreshold}
+\title{enve recplot2 windowDepthThreshold}
+\description{Identifies the threshold below which windows should be identified as
+variable or absent.}
+\usage{enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE, 
+    significance = 0.05)}
+\arguments{
+  \item{rp}{Recruitment plot, an `enve.RecPlot2` object.}
+  \item{peak}{Peak, an `enve.RecPlot2.Peak` object. If list, it is assumed to be a
+list of `enve.RecPlot2.Peak` objects, in which case the core peak is
+used (see `enve.recplot2.corePeak`).}
+  \item{lower.tail}{If FALSE, it returns windows significantly above the peak in
+sequencing depth.}
+  \item{significance}{Significance threshold (alpha) to select windows.}
+}
+
+\value{Returns a float. The units are depth if the peaks were estimated in
+linear scale, or log-depth otherwise (`peak$log`).}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

data/utils/enveomics/enveomics.R/man/enve.truncate.Rd

@@ -0,0 +1,22 @@
+\name{enve.truncate}
+\alias{enve.truncate}
+\title{enve truncate}
+\description{Removes the `n` highest and lowest values from a vector, and applies a
+summary function. The value of `n` is determined such that the central
+range is used, corresponding to the `f` fraction of values.}
+\usage{enve.truncate(x, f = 0.95, FUN = mean)}
+\arguments{
+  \item{x}{A vector of numbers.}
+  \item{f}{The fraction of values to retain.}
+  \item{FUN}{Summary function to apply to the vectors. To obtain the truncated
+vector itself, use `c`.}
+}
+
+\value{Returns the summary (`FUN`) of the truncated vector.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd

@@ -3,9 +3,9 @@
 \title{plot enve RecPlot2}
 \description{Plots an `enve.RecPlot2` object.}
 \usage{\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow = 2), 
-    widths = c(1, 7, 2), heights = c(1, 2), palette = grey((100:0)/100), 
-    underlay.group = TRUE, peaks.col = "darkred", use.peaks, 
-    id.lim = range(x$id.breaks), pos.lim = range(x$pos.breaks), 
+    panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2), 
+    palette = grey((100:0)/100), underlay.group = TRUE, peaks.col = "darkred", 
+    use.peaks, id.lim = range(x$id.breaks), pos.lim = range(x$pos.breaks), 
     pos.units = c("Mbp", "Kbp", "bp"), mar = list(`1` = c(5, 
         4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1), 1, 5), 
         4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 
@@ -28,10 +28,16 @@ where:
 3: identity histogram,
 4: Populations histogram (histogram of sequencing depths),
 5: Color scale for the counts matrix (vertical),
-6: Color scale of the counts
-matrix (horizontal). Only panels indicated here will be plotted. To
-plot only one panel simply set this to the number of the panel you
-want to plot.}
+6: Color scale of the counts matrix (horizontal)
+Only panels indicated here will be plotted. To plot only one panel
+simply set this to the number of the panel you want to plot.}
+  \item{panel.fun}{List of functions to be executed after drawing each panel. Use the
+indices in `layout` (as characters) as keys. Functions for indices
+missing in `layout` are ignored. For example, to add a vertical line
+at the 3Mbp mark in both the position histogram and the counts matrix:
+`list('1'=function() abline(v=3), '2'=function() abline(v=3))`.
+Note that the X-axis in both panels is in Mbp by default. To change
+this behavior, set `pos.units` accordingly.}
   \item{widths}{Relative widths of the columns of `layout`.}
   \item{heights}{Relative heights of the rows of `layout`.}
   \item{palette}{Colors to be used to represent the counts matrix, sorted from no hits

data/utils/enveomics/enveomics.R/man/z$-methods.Rd

@@ -12,16 +12,15 @@
 \describe{
 
 \item{\code{signature(x = "enve.GrowthCurve")}}{
-%%  ~~describe this method here~~
+enve.GrowthCurve, a growth curve
 }
 
 \item{\code{signature(x = "enve.RecPlot2")}}{
-%%  ~~describe this method here~~
+enve.RecPlot2, a recruitment plot
 }
 
 \item{\code{signature(x = "enve.RecPlot2.Peak")}}{
-%%  ~~describe this method here~~
+enve.RecPlot2.Peak, a peak from a recruitment plot
 }
 }}
 \keyword{methods}
-\keyword{ ~~ other possible keyword(s) ~~ }

data/utils/subclade/runner.rb

@@ -24,6 +24,10 @@ class MiGA::SubcladeRunner
   # Launch the appropriate analysis
   def go!
     return if project.type == :metagenomes
+    unless @project.dataset_names.any? { |i| @project.dataset(i).is_ref? }
+      FileUtils.touch(File.expand_path('miga-project.empty', @home))
+      return
+    end
     Dir.chdir home
     Dir.mktmpdir do |tmp_dir|
       @tmp = tmp_dir

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.9.0
+  version: 0.3.9.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-07 00:00:00.000000000 Z
+date: 2019-03-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -110,6 +110,7 @@ files:
 - actions/daemon.rb
 - actions/date.rb
 - actions/doctor.rb
+- actions/edit.rb
 - actions/files.rb
 - actions/find.rb
 - actions/get.rb
@@ -118,6 +119,7 @@ files:
 - actions/ls.rb
 - actions/ncbi_get.rb
 - actions/new.rb
+- actions/next_step.rb
 - actions/plugins.rb
 - actions/rm.rb
 - actions/run.rb
@@ -161,6 +163,7 @@ files:
 - scripts/assembly.bash
 - scripts/cds.bash
 - scripts/clade_finding.bash
+- scripts/d.bash
 - scripts/distances.bash
 - scripts/essential_genes.bash
 - scripts/haai_distances.bash
@@ -169,6 +172,7 @@ files:
 - scripts/mytaxa.bash
 - scripts/mytaxa_scan.bash
 - scripts/ogs.bash
+- scripts/p.bash
 - scripts/project_stats.bash
 - scripts/read_quality.bash
 - scripts/ssu.bash
@@ -285,6 +289,7 @@ files:
 - utils/enveomics/Scripts/CharTable.classify.rb
 - utils/enveomics/Scripts/EBIseq2tax.rb
 - utils/enveomics/Scripts/FastA.N50.pl
+- utils/enveomics/Scripts/FastA.extract.rb
 - utils/enveomics/Scripts/FastA.filter.pl
 - utils/enveomics/Scripts/FastA.filterLen.pl
 - utils/enveomics/Scripts/FastA.filterN.pl
@@ -292,10 +297,12 @@ files:
 - utils/enveomics/Scripts/FastA.gc.pl
 - utils/enveomics/Scripts/FastA.interpose.pl
 - utils/enveomics/Scripts/FastA.length.pl
+- utils/enveomics/Scripts/FastA.mask.rb
 - utils/enveomics/Scripts/FastA.per_file.pl
 - utils/enveomics/Scripts/FastA.qlen.pl
 - utils/enveomics/Scripts/FastA.rename.pl
 - utils/enveomics/Scripts/FastA.revcom.pl
+- utils/enveomics/Scripts/FastA.sample.rb
 - utils/enveomics/Scripts/FastA.slider.pl
 - utils/enveomics/Scripts/FastA.split.pl
 - utils/enveomics/Scripts/FastA.split.rb
@@ -309,6 +316,7 @@ files:
 - utils/enveomics/Scripts/FastQ.tag.rb
 - utils/enveomics/Scripts/FastQ.test-error.rb
 - utils/enveomics/Scripts/FastQ.toFastA.awk
+- utils/enveomics/Scripts/GFF.catsbj.pl
 - utils/enveomics/Scripts/GenBank.add_fields.rb
 - utils/enveomics/Scripts/HMM.essential.rb
 - utils/enveomics/Scripts/HMMsearch.extractIds.rb
@@ -440,8 +448,10 @@ files:
 - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
+- utils/enveomics/enveomics.R/man/enve.truncate.Rd
 - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
 - utils/enveomics/enveomics.R/man/growth.curves.Rd
 - utils/enveomics/enveomics.R/man/phyla.counts.Rd
@@ -496,7 +506,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.2
+rubyforge_project: 
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: MiGA