Class: BigSimon::Utils

Inherits:
Object
  • Object
show all
Defined in:
lib/big_simon/utils.rb

Overview

TODO:

These don’t have unit tests yet.

Note:

Skips any duplicate IDs. Only keeps the first one.

Class Method Summary collapse

Class Method Details

.check_file!(fname) ⇒ Object 



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# File 'lib/big_simon/utils.rb', line 5

def self.check_file! fname
  Rya::AbortIf.abort_if fname && !File.exist?(fname),
                        "#{fname} doesn't exist!  Try big_simon --help for help."
end

.check_opt!(opts, arg) ⇒ Object 



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# File 'lib/big_simon/utils.rb', line 10

def self.check_opt! opts, arg
  Rya::AbortIf.abort_unless opts.send(:fetch, "#{arg}_given".to_sym),
                            "You must specify --#{arg.to_s.tr('_', '-')}.  Try big_simon --help for help."
end

.rcode(fnames) ⇒ Object 



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# File 'lib/big_simon/utils.rb', line 15

def self.rcode fnames
  functions = %Q|
  library(reshape2)
library(gplots)
library(RColorBrewer)

file.join <- function(...) {
paste(..., sep="/")
}

draw.heatmap <- function(infname, outfname) {
dat <- read.table(infname, header=T, sep="\t")

wide.dat <- dcast(dat, host ~ virus, value.var="score")

hosts <- wide.dat[, 1]
scores <- wide.dat[, 2:ncol(wide.dat)]
scores.numeric <- apply(scores, 2, as.numeric)

scores.matrix <- as.matrix(scores.numeric)

rownames(scores.matrix) <- hosts

palette <- "YlOrBr"
col <- colorRampPalette(brewer.pal(n=9, palette))(n = 25)
size <- 0.75

pdf(outfname, height=5, width=8)

heatmap.2(scores.matrix,
          trace="none", ## Disable those wonky lines.
          col=col, ## Set the color.

          ## Size opts
          margins=c(11, 11), cexRow=size, cexCol=size,

          ## Key labeling
          key.xlab="Score")

invisible(dev.off())
}

|

  drawing = fnames.map do |in_fname, out_fname|
    %Q{

draw.heatmap("#{in_fname}", "#{out_fname}")
}
  end.join

  [functions, drawing].join "\n"
end

.scale_log_likelihood(ll) ⇒ Object 



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# File 'lib/big_simon/utils.rb', line 69

def self.scale_log_likelihood ll
  1 - Math.exp(ll)
end

.set_up_tmp_dirs(fastas, tmpdir, which) ⇒ Object

Note:

I also rename all the sequences in the tmp fasta files with the new ID.



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# File 'lib/big_simon/utils.rb', line 74

def self.set_up_tmp_dirs fastas, tmpdir, which
  Object::FileUtils.mkdir_p tmpdir

  seq_lengths = {}

  name_map = {}
  all_ids  = Set.new

  seq_num = -1
  fastas.each do |fname|
    ParseFasta::SeqFile.open(fname).each_record do |rec|
      if all_ids.include? rec.id
        Rya::AbortIf.logger.warn { "#{rec.id} was seen more than one time!  Duplicate organism IDs are not allowed, so we will only keep the first one." }
      else
        all_ids << rec.id

        seq_num += 1

        new_id           = "#{which}_#{seq_num}"
        name_map[new_id] = rec.id

        outfname = File.join tmpdir, "#{new_id}.fa"

        seq_lengths[new_id] = rec.seq.length

        File.open(outfname, "w") do |f|
          f.puts ">#{new_id}\n#{rec.seq}" # TODO HERE
        end
      end
    end
  end

  [name_map, all_ids, seq_lengths]
end

.strip_suffix(fname) ⇒ Object 



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# File 'lib/big_simon/utils.rb', line 109

def self.strip_suffix fname
  fname.sub /.fasta$|.fa$/, ""
end