yannickwurm

"<h1>ERROR: incorrect number of sequences found.</h1
<p>Dear user,</p>
<p><strong>you requested #{sequenceids.length} sequences</strong> 
   with the following identifiers:  <emph>#{sequenceids.join(', ')}</emph>, 
   from the following databases:<emph>#{retrieval_databases.join(', ')}</emph>.
</p>
<p/>
<p><strong>But we found #{found_sequences_count} sequences.</strong>. 
   This is <em>#{found_sequences_count > sequenceids.length ? 'more' : 'less'}</em>
   sequences than expected.</p>

yannickwurm

#!/usr/bin/env ruby
# (copy) Yannick Wurm - google me.
# All right reserved. 

help = "Usage: \n" + 
       "      #{$0} MySequences_R1.fastq MySequences_R2.fastq > MySequences_R1R2pasted.fastq\n" + 
       "Joins two paired reads into a single megaread. Can be helpful for deduplication.\n" +
       "The two fastq files must have reads in the same order. Some error checking is performed.\n"

yannickwurm

    def YWSystemTools.runMultithreaded(commandArray)
        # runs commands on N processors at a time - can take more jobs & launches them sequentially.

        if commandArray.length > 1
            $log.info("#{commandArray.length} commands to run")
        elsif commandArray.length == 1
            $log.warn("only one command!")
        else
            raise ArgumentError, 'No commands to run!'
        end

yannickwurm

        ('proc00001'..'proc00024').each do |processor|
            threads << Thread.new(processor) do |threadid|                                                          
                until commandArray.empty?
                    commandToRun = commandArray.pop
                    $log.info('running:' + commandToRun)
##                    %x[#{commandToRun}] 
                    stdout = %x[#{commandToRun}]
                    print(stdout)
                end
            end

yannickwurm

    def YWSystemTools.number_of_processors
        if RUBY_PLATFORM =~ /linux/
            cpuinfo = IO.readlines("/proc/cpuinfo").delete_if{|x| x.index("processor")==nil}
            return cpuinfo.length
        elsif RUBY_PLATFORM =~ /darwin/
            return `sysctl -n hw.logicalcpu`.to_i
        elsif RUBY_PLATFORM =~ /win32/
            #            this works for windows 2000 or greater
            require 'win32ole'
            wmi = WIN32OLE.connect("winmgmts://")

yannickwurm

  def parse(signalp_hash, open_reading_frames_condensed, motif)
      signalp_with_seq = {}
      signalp_hash.each do |id, h|
          current_orf = open_reading_frames_condensed[id]
          sequence = current_orf.to_s.gsub('["', '').gsub('"]', '')
          sp_clv = h[0][:cut_off].to_i - 1
          signalp = sequence[0,sp_clv]
          seq_end = sequence[sp_clv+1, sequence.length - (sp_clv+1)]
           if seq_end.match(/#{motif}/)
                signalp_with_seq[id + "~- S.P. Cleavage Site: #{sp_clv}:" \

yannickwurm

mkdir converted
find . -regex .*mp3 | ruby -pe 'gsub(".mp3", "")' | xargs -I __ ffmpeg -i __.mp3  -ss 0 -t 30  -ac 1 -ab 256000 -f mp4 -acodec libfaac -y __.m4r
 
 #important: limit to 30 seconds otherwise iTunes won't transfer it to iphone. 
 
 

yannickwurm

-bash-4.1$ uname -a
Linux sm11 2.6.32-431.1.2.el6.x86_64 #1 SMP Thu Dec 12 13:59:19 CST 2013 x86_64 x86_64 x86_64 GNU/Linux
-bash-4.1$ ruby -v
ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux]
-bash-4.1$ which ruby
~/.rbenv/shims/ruby
-bash-4.1$ gem environment
RubyGems Environment:
  - RUBYGEMS VERSION: 1.8.23
  - RUBY VERSION: 1.9.2 (2011-07-09 patchlevel 290) [x86_64-linux]

yannickwurm

Score	 Expect	 Identities	 Positives	 Gaps	 Frame
34.97 (70)	 0.163	 13/27 (48.15%)	 19/27 (70.37%)	 0/27 (0.00%)	 (3/-2)
Query   111    LVLGLIGNIFLMYYFVKCLLKYFI*KI 191
               LVL L+ N+ + YY + CLL YF+ +I
Subject 120133 LVLKLVDNLAIYYYIILCLLLYFLIRI 120213

yannickwurm

Failed to load resource: the server responded with a status of 401 (Unauthorized) http://afra.sbcs.qmul.ac.uk/lib/jquery/jquery.js?bust=1409565929178
Uncaught Error: Script error for: jquery
http://requirejs.org/docs/errors.html#scripterror require.js:138
Failed to load resource: net::ERR_FAILED chrome-extension://invalid/
less: XHR: Getting 'http://afra.sbcs.qmul.ac.uk/styles.less?bust=1409565929178' lessc.js?bust=1409565929178:6297
less: XHR: Getting 'http://afra.sbcs.qmul.ac.uk/lib/bootstrap/less/variables.less' lessc.js?bust=1409565929178:6297
less: XHR: Getting 'http://afra.sbcs.qmul.ac.uk/lib/bootstrap/less/mixins.less' lessc.js?bust=1409565929178:6297
less: XHR: Getting 'http://afra.sbcs.qmul.ac.uk/lib/bootstrap/less/normalize.less' lessc.js?bust=1409565929178:6297
less: XHR: Getting 'http://afra.sbcs.qmul.ac.uk/lib/bootstrap/less/scaffolding.less' lessc.js?bust=1409565929178:6297