shujishigenobu

##
# to_dokuwiki_table.rb
# convert tab-delimited text to dokuwiki table

file = ARGV[0]
File.open(file).each do |l|
  a = l.chomp.split(/\t/)
  puts "|" + a.map{|x| "#{x} "}.join("|") + "|"
end

shujishigenobu

#!/usr/bin/env ruby

require 'rubygems'
require 'active_support/core_ext/hash/conversions'
require 'open-uri'
require 'json'
require 'yaml'
require 'pp'

infile = ARGV[0]

shujishigenobu

cosine.coef <- function(x,y){
  a <- sum(na.omit(x * y)) / sqrt(sum(na.omit(x)^2) * sum(na.omit(y)^2))
  return(a)
}

cosine.table <- function(x) {
  numberOfPoints <- ncol(x)
  columnNames    <- colnames(x)
  distanceTable  <- matrix(data = NA, nrow = numberOfPoints, ncol = numberOfPoints,
                         dimnames = list( columnNames, columnNames ) )

shujishigenobu

require 'bio'
include Bio

#require 'pp'
#alias :p :pp

ref_proteome_file = ARGV[0]
# || "/home/DB/public/processed/OrthoDB/OrthoDB7/blastdb/DMELA.Drosophila_melanogaster.fas")
blast_res_file = ARGV[1]
# || "BLAST_DMELA/RsGM3.evm.out.combined.pep.vs.DMELA.Drosophila_melanogaster.fas.blastp.fmt7c.txt")

shujishigenobu

#!/usr/bin/ruby

$pp = true # pretty print
$head = true # display header
$targetdir = ( ARGV[0] || "fastqc")


files = Dir["#{$targetdir}/*_fastqc/fastqc_data.txt"]

shujishigenobu

### Parse command-line options
require 'optparse'
opt = OptionParser.new
opt.on('-i', '--in FASTA', 'predicted protein files in fasta format [required]') {|v| $pepf = v}
opt.on('-d', '--db BLASTDB', 'blastdb [required]') {|v| $blastdb = v}
opt.on('-m', '--min [MIN_LEN]', 'min aa length to predict [default:50]') {|v| $min_len = v.to_i}
opt.on('-h', '--help', 'show this message'){
  puts opt; exit
}

shujishigenobu

!/bin/ruby

#=== config
MAX_MEMORY = 30000000000
#===


$sam = ARGV[0]

bam_unsorted = File.basename($sam, '.sam') + '.unsorted.bam'

shujishigenobu

#===
# taxpath.rb
# Obtain full path of lineage from root to target species

### conf ###
taxtab = "/home/DB/public/processed/NCBI/taxonomy/taxdump/nodes.dmp"
nametab = "/home/DB/public/processed/NCBI/taxonomy/taxdump/names.dmp"
###

infile = ARGV[0]

shujishigenobu

#===
# nr_taxinfo.rb
#
# Reading tab-delimited tables, retrieve taxonomy information.
# It works only with NCBI nr database.
# Three columns, tax_id, scientific_name and common_name, are added.

$infile = ARGV[0]
$blastdb = ARGV[1]
$keypos = (ARGV[2] || 1).to_i

shujishigenobu

$infile = ARGV[0]
$blastdb = ARGV[1]
$keypos = (ARGV[2] || 1).to_i

=begin
counter = Hash.new(0)
File.open($infile).each do |l|
  next if /^\#/.match(l)
  a = l.chomp.split(/\t/)
  tophit = a[2]