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MatthewRalston / Random_subsample.xml
Last active Aug 29, 2015
Galaxy tool for subsampling a fastq file.
View Random_subsample.xml
<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 $paired_list_output.reverse
</command>
@MatthewRalston
MatthewRalston / summarize_fastqc.xml
Created Jul 15, 2015
Galaxy tool for summarizing fastqc information
View summarize_fastqc.xml
<tool name="Summarize FastQC" id="summarizeFastQCMetrics" version="0.0.1">
<description>summarizes data from FastQC</description>
<command>
#def pairfunc($theList)
#set $left = []
#set $right = []
#for $file1, $file2 in $theList
#$left.append(str($file1))
#$right.append(str($file2))
@MatthewRalston
MatthewRalston / log.conf
Created Oct 28, 2015
Python logging: configuration file and root_logger setup.
View log.conf
import logging
import logging.config
def get_root_logger(loglevel, logfile=None, log_config="log.conf"):
# Requires 'import logging' and 'import logging.config'
def log_level(loglevel):
case = {"DEBUG": logging.DEBUG,
"INFO": logging.INFO,
"WARNING": logging.WARNING,
@MatthewRalston
MatthewRalston / example.rb
Created Nov 16, 2015
log4r YAML configuration
View example.rb
require 'log4r'
require 'log4r/yamlconfigurator'
include Log4r
ycfg = YamlConfigurator
ycfg["LOGFILE"] = "/home/matt/logs/myapp.log"
ycfg.load_yaml_file("/home/matt/.config/ruby/logger.yaml")
root_logger = Logger['root_logger']
@MatthewRalston
MatthewRalston / Autogen.log
Created Nov 24, 2015
Slurm-drmaa compilation logs
View Autogen.log
>./autogen.sh
checking for aclocal... yes
checking for autoheader... yes
checking for autoconf... yes
checking for libtoolize... yes
checking for automake... yes
running aclocal -I m4 (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running libtoolize --automake --copy --force (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running autoheader --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
running automake --foreign --add-missing --copy --warnings=all (/opt/slurm-drmaa-slurm-drmaa-1.2.0-clusters)
View .bash_profiile
#set -x
##
# Your previous /Users/Matthew/.bash_profile file was backed up as /Users/Matthew/.bash_profile.macports-saved_2013-04-01_at_23:07:38
##
export PATH=/usr/local/bin/:$PATH
# MacPorts Installer addition on 2013-04-01_at_23:07:38: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:/Users/Matthew/Documents/Bash_scripts:/Applications/circos-0.66/bin/:$PATH
@MatthewRalston
MatthewRalston / fancy_scientific.R
Created Mar 21, 2016
Scientific notation (5x10^5)
View fancy_scientific.R
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)
}
View hamming_match.py
'''
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
MatthewRalston / ml-ruby.md
Created May 5, 2016 — forked from gbuesing/ml-ruby.md
Resources for Machine Learning in Ruby
View ml-ruby.md

Resources for Machine Learning in Ruby

Gems

View Hello.rb
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:
You can’t perform that action at this time.