MatthewRalston

<tool name="Random Subsample" id="subsample_fastq" version="0.0.1">
  <description>Subsamples a fastq file</description>
  <command>

    RandomSubFq -w $readsRequested
    -i $paired_fastq_files.forward
    -i $paired_fastq_files.reverse
    -o $paired_list_output.forward
    -o $paired_list_output.reverse
  </command>

MatthewRalston

<tool name="Summarize FastQC" id="summarizeFastQCMetrics" version="0.0.1">
  <description>summarizes data from FastQC</description>
  <command>

    #def pairfunc($theList)
    #set $left = []
    #set $right = []
    #for $file1, $file2 in $theList
        #$left.append(str($file1))
        #$right.append(str($file2))

MatthewRalston

import logging
import logging.config

def get_root_logger(loglevel, logfile=None, log_config="log.conf"):
    # Requires 'import logging' and 'import logging.config'

    def log_level(loglevel):
        case = {"DEBUG": logging.DEBUG,
                "INFO": logging.INFO,
                "WARNING": logging.WARNING,

MatthewRalston

require 'log4r'
require 'log4r/yamlconfigurator'
include Log4r

ycfg = YamlConfigurator
ycfg["LOGFILE"] = "/home/matt/logs/myapp.log"
ycfg.load_yaml_file("/home/matt/.config/ruby/logger.yaml")
root_logger = Logger['root_logger']

MatthewRalston

>./autogen.sh 
checking for aclocal... yes
checking for autoheader... yes
checking for autoconf... yes
checking for libtoolize... yes
checking for automake... yes
running aclocal -I m4 (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running libtoolize --automake --copy --force (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running autoheader --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running automake --foreign --add-missing --copy --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)

MatthewRalston

fancy_scientific <- function(l) {
     # turn in to character string in scientific notation
     l <- format(l, scientific = TRUE)
     # quote the part before the exponent to keep all the digits
     l <- gsub("^(.*)e", "'\\1'e", l)
     # turn the 'e+' into plotmath format
     l <- gsub("e", "%*%10^", l)
     # return this as an expression
     parse(text=l)
}

MatthewRalston

'''
When you want to match files that only differ by one character: sample_1.fastq.gz sample_2.fastq.gz
'''
def is_hamming_match(seq1, seq2):
  if len(seq1) == len(seq2): # The sequences must be of equal length
    zipped = zip(seq1, seq2)
    is_mismatch = list([c1 != c2 for c1, c2 in zipped])
    if sum(is_mismatch) == 1: # The sequences must have only one mismatch
      mismatches = list([[c1, c2] for c1, c2 in zipped if c1 != c2])
      if mismatches[0] == ['1', '2'] or mismatches[0] == ['2', '1']:  # The mismatch must only be the numbers 1 and 2

MatthewRalston

Resources for Machine Learning in Ruby

Gems

• liblinear-ruby: Ruby interface to LIBLINEAR using SWIG

• classifier-reborn: Bayesian and LSI classification
  dependencies: GSL

MatthewRalston

partner = Object.new
def my_most_sincere_apology
  "I'm sorry for everything that I've done. But when I call you never seem to be home."
end

try:
  1000.times do |t|
    partner.call(:my_most_sincere_apology)
  end
catch e:

MatthewRalston

Sample service script for debianoids

Look at LSB init scripts for more information.

Usage

Copy to /etc/init.d:

# replace "$YOUR_SERVICE_NAME" with your service's name (whenever it's not enough obvious)