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• 50 sequences in one line

  - by user343934

  I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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• Answers to Conference Revenue Tweet Questions

  - by D'Arcy Lussier

  Originally posted on: http://geekswithblogs.net/dlussier/archive/2014/05/27/156612.aspxI tweeted this the other day… …and I had some people tweet back questioning/asking about the profit number. So here’s how I came to that figure. Total Revenue Let’s talk total revenue first. This conference has a huge list of companies/organizations paying some amount for sponsorship. Platinum ($1500) x 5 = $7500 Gold ($1000) x 3 = $3000 Silver ($500) x 9 = $4500 Bronze ($250) x 13 = $3250 There’s also a title sponsor level but there’s no mention of how much that is…more than $1500 though, so let’s just say $2500. Total Sponsorship Revenue: $20750.00 For registrations, this conference is claiming over 300 attendees. We’ll just calculate at 300 and the discounted “member rate” – $249. Total Registration Revenue: $74700.00 Booth space is also sold for a vendor area, but let’s just leave that out of the calculation. Total Event Revenue: $95450.00 Now that we know how much money we’re playing with, let’s knock out the costs for the event. Total Costs Hard Costs Audio/Visual Services $2000 Conference Rooms (4 Breakouts + Plenary) $2500 Insurance $700 Printing/Signage $1500 Travel/Hotel Rooms $2000 Keynotes $2000 So let’s talk about these hard costs first. First you may be asking about the Audio Visual. Yes those services can be that high, actually higher. But since there’s an A/V company touted as the official A/V provider, I gotta think there’s some discount for being branded as such. Conference rooms are actually an inflated amount of $500 per. Venues make money on the food they sell at events, not on room rentals. The more food, the cheaper the rooms tend to be offered at. Still, for the sake of argument, let’s set the rooms at $500 each knowing that they could be lower. For travel and hotel rooms…it appears that most of the speakers at this conference are local, meaning there’s no travel or hotel cost. But a few of them I wasn’t too sure…so let’s factor in enough to cover two outside speakers (airfare and hotel). There are two keynotes for this event and depending on the event those may be paid gigs. I’m not sure if they are or not, but considering the closing one is a comedian I’m going to add some funds here for that just in case. Total Hard Costs: $10700 Now that the hard costs are out of the way, let’s talk about the food costs. Food Costs The conference is providing a continental breakfast (YEEEESH!), some level of luncheon, and I have to assume coffee breaks in between. Let’s look at those costs. Continental Breakfast $12 per person Lunch Buffet $18 per person Coffee Breaks (2) $6 per person (or $3 a cup) Snacks (2) $10 per person (or $5 each) Note that the lunch buffet assumes a *good* lunch buffet – two entrees, starch, vegetable, salads, and bread. Not sure if there’ll be snacks during coffee breaks but let’s assume so. Total Food Cost Per Person: $46 Food Cost: $14950 Gratuity: $2691 Total Food Cost: $17641 Total food cost is based on the $46 per person cost x 325. 300 for attendance, 12 for speakers, extra 13 for volunteers/organizers. Gratuity is 18%. Grand Totals So let’s sum things up here. Total Costs Hard Costs: $10700.00 Food Costs: $17641.00 Total:          $28341.00 Taxes:         $3685.00 Grand Total  $32026.00 Total Revenue Sponsorship  $20750 Registration   $74700 Grand Total   $95450.00 Total Profit $63424.00 Now what if the registration numbers were lower and they only got 100 people to show up. In that scenario there’d still be a profit of just under $26000. Closing Comments A couple of things to note: - I haven’t factored in anything for prizes. Not sure if any will be given out - We didn’t add in the booth space revenue - We’re assuming speakers aren’t getting paid, but even if they were at the high end its $12000 ($1000 per session), which is probably an inflated number for local speakers. - Note that all registrations were set to the “member” discounted price. The non-member registration price is higher. There is also an option for those that just want to show up for the opening keynote. There you have it! Let me know if you have any questions. D

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• Cross browser (chrome/firefox) trying to get top-pos defined in percentage as pixels

  - by Cinaird

  I have a problem whit cross browser output, I'm trying to get the top and left css attribute of a div, but firefox gives me the exact pixel position and Chrome give me the percentage. Example: http://web.cinaird.se/pdf/test.htm CSS #mix{ position:absolute; top: 10px; left: 45%; background-color:#f0f; } jQuery css top: " + $("#mix").css("top") + " <br/>css left: " + $("#mix").css("left") Output Firefox (and IE8): css top: 10px css left: 267.3px Chrome: css top: 10px css left: 45% is there any way to get the same result for both (all) browsers? I would prefer to get a pixel value without any major calculation

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• VS2005 project has dependency that is not built

  - by Eyal

  I have VS2005 solution that contains many projects and dependencies (some C++, some C#) - in the past it compiled successfully. when I rebuild all the solution it fails on a project claiming dll is missing (dll that was needed to built before according to dependency). the thing is that from time to time it fails on random project (not all the time the same project). I'm not sure it is meaningful but I see in output console Deleting intermediate and output files for project doesn't VS2005 go according to "Project Build Order" and ReBuild every project starting with its dependencies?

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• How to use > in an xargs command?

  - by jesse

  I want to find a bash command that will let me grep every file in a directory and write the output of that grep to a separate file. My guess would have been to do something like this ls -1 | xargs -I{} "grep ABC '{}' > '{}'.out" but, as far as I know, xargs doesn't like the double-quotes. If I remove the double-quotes, however, then the command redirects the output of the entire command to a single file called '{}'.out instead of to a series of individual files. Does anyone know of a way to do this using xargs? I just used this grep scenario as an example to illustrate my problem with xargs so any solutions that don't use xargs aren't as applicable for me.

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• How do you Remove an Invalid Remote Branch Reference from Git?

  - by Casey

  In my current repo I have the following output: $ git branch -a * master remotes/origin/master remotes/public/master I want to delete 'remotes/public/master' from the branch list: $ git branch -d remotes/public/master error: branch 'remotes/public/master' not found. Also, the output of 'git remote' is strange, since it does not list 'public': $ git remote show origin How can I delete 'remotes/public/master' from the branch list? Update, tried the 'git push' command: $ git push public :master fatal: 'public' does not appear to be a git repository fatal: The remote end hung up unexpectedly Solution: The accepted answer had the solution at the bottom! git gc --prune=now

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• the problem about different treatment to __VA_ARGS__ when using VS 2008 and GCC

  - by liuliu

  I am trying to identify a problem because of an unusual usage of variadic macros. Here is the hypothetic macro: #define va(c, d, ...) c(d, __VA_ARGS__) #define var(a, b, ...) va(__VA_ARGS__, a, b) var(2, 3, printf, “%d %d %d\n”, 1); For gcc, the preprocessor will output printf("%d %d %d\n", 1, 2, 3) but for VS 2008, the output is printf, “%d %d %d\n”, 1(2, 3); I suspect the difference is caused by the different treatment to VA_ARGS, for gcc, it will first expand the expression to va(printf, "%d %d %d\n", 1, 2, 3), and treat 1, 2, 3 as the VA_ARGS for macro va. But for VS 2008, it will first treat b as VA_ARGS for macro va, and then do the expansion. Which one is correct interpretation for C99 variadic macro? or my usage falls into an undefined behavior?

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• c#: RedirectStandardOutput prevents exit exception?

  - by user1743977

  All I want is to redirect standard output of a process to a file. Sounds easy, but everything I tried doesn't work: 1) putting a dos-style redirection in the list of arguments (e.g. "param1 param2 output.txt") doesn't work, 2) using RedirectStandardOutput = true works, BUT, apparently the process does not through an exception when it exists. So the handler defined via process.Exited += ... doesn't catch anything. To be clear, once I remove the 'RedirectStandardOutput = true ' statement, it DOES catch an exception. What am I doing wrong ? Thanks, Ofer

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• How to convert mkv to dvd or avi

  - by nathanvda

  I have some mkv files, and while Totem plays them perfectly, when i use Devede to burn them to dvd it all gets messed up: the video is ok, but the audio is out of sync. I did see that Devede does write my dixv avi files correctly to disk. So i am thinking what the best way could be to convert my mkv for playback on dvd? I was thinking maybe converting them to avi first? But i did not find a good way for that to happen. What do you suggest?

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• how to merge file lines having the same first word in python?

  - by user1377135

  I have written a program to merge lines in a file containing the same first word in python. However I am unable to get the desired output. Can anyone please suggest me the mistake in my program? input "file.txt" line1: a b c line2: a b1 c1 line3: d e f line4: i j k line5: i s t line6: i m n ` output a b c a b1 c1 d e f i j k i s t i m n my code a = [line.split() for line in open('file.txt')] L=[] for i in range(0,len(a)): j=i while True: if a[j][0] == a[j+1][0]: L.append(a[j]) L.append(a[j+1]) j=j+2 else: print a[i] print L break

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• Removing surrounding noises from voice recording

  - by Peak Reconstruction Wavelength

  I have a wave file whose frequency spectrum looks like this. http://i.stack.imgur.com/2rRaS.png It contains audio, which I want to keep while removing the rest. The problem is that the surround noise changes, just those distinct voice patterns remain. I marked the voice patterns for clarity: http://i.stack.imgur.com/eLkBl.png What could an algorithm look like / a workflow in adobe audition look like that removes everything but the voice patterns? I think that the main characteristic is the line-shaped form over time. Loudness alone is not enough as the noise is loud aswell.

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• SQL: without a cursor, how to select records making a unique integer id (identity like) for dups?

  - by Dr. Zim

  If you have the select statement below where the PK is the primary key: select distinct dbo.DateAsInt( dateEntered) * 100 as PK, recordDescription as Data from MyTable and the output is something like this (the first numbers are spaced for clarity): PK Data 2010 01 01 00 New Years Day 2010 01 01 00 Make Resolutions 2010 01 01 00 Return Gifts 2010 02 14 00 Valentines day 2010 02 14 00 Buy flowers and you want to output something like this: PK Data 2010 01 01 01 New Years Day 2010 01 01 02 Make Resolutions 2010 01 01 03 Return Gifts 2010 02 14 01 Valentines day 2010 02 14 02 Buy flowers Is it possible to make the "00" in the PK have an "identity" number effect within a single select? Otherwise, how could you increment the number by 1 for each found activity for that date? I am already thinking as I type to try something like Sum(case when ?? then 1 end) with a group by.

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• How to set the default Microphone

  - by kmh42

  I am using an external Web-cam with a build-in Microphone. When I am using Skype or some other Software it doesn’t recognise the Microphone automatically. So I always have to activate it myself in the Audio Settings. How can I avoid this and set it as default Web-cam. This PC doesn't have another Webcam or Mic. And the Web-cam is always pluged in. Ubuntu 12.04 beta with latest updates (I also had this problems with 10.04) Logitech, Inc. Web-cam B500

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• How to run a jar file in hadoop

  - by Arihant

  I have created a jar file using the java file from this blog using following statements javac -classpath /usr/local/hadoop/hadoop-core-1.0.3.jar -d /home/hduser/dir Dictionary.java /usr/lib/jvm/jdk1.7.0_07/bin/jar cf Dictionary.jar /home/hduser/dir Now i have tried running this jar in hadoop by hit and trial of various commands 1hduser@ubuntu:~$ /usr/local/hadoop/bin/hadoop jar Dictionary.jar Output: Warning: $HADOOP_HOME is deprecated. RunJar jarFile [mainClass] args... 2.hduser@ubuntu:~$ /usr/local/hadoop/bin/hadoop jar Dictionary.jar Dictionary Output: Warning: $HADOOP_HOME is deprecated. Exception in thread "main" java.lang.ClassNotFoundException: Dictionary at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:423) at java.lang.ClassLoader.loadClass(ClassLoader.java:356) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at org.apache.hadoop.util.RunJar.main(RunJar.java:149) How can i run the jar in hadoop? I have the right DFS Locations as per needed by my program.

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• Create a screencast in a low end PC, but fast (maybe by sacrificing compression ?)

  - by josinalvo

  As the title suggests, I am asking a lot. We've been trying to generate some screencasts on my eeepc. recordmydesktop is doing the job decently, but only if allowed time to "compile" the video afterwards. If we ask it to do "on the fly", video and audio get out of sync. Now, we are creating many screencasts as practice (and like to watch them after, to criticize). Reducing quality is undesirable, because eventually a good practice run becomes the one we'll release. So we'd like a way to do screencasts "on the fly", with decent quality, on the low end machine. As nothing is ever free, we are willing to sacrifice: we don't care too much about compression: 20GB for a 15min video is acceptable

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• The Most Important Person Is the One that Keeps Your PC Running [Comic]

  - by The Geek

  Fixing people’s computers usually makes them appreciate you more, though this might be a little too far. Latest Features How-To Geek ETC How To Create Your Own Custom ASCII Art from Any Image How To Process Camera Raw Without Paying for Adobe Photoshop How Do You Block Annoying Text Message (SMS) Spam? How to Use and Master the Notoriously Difficult Pen Tool in Photoshop HTG Explains: What Are the Differences Between All Those Audio Formats? How To Use Layer Masks and Vector Masks to Remove Complex Backgrounds in Photoshop Bring Summer Back to Your Desktop with the LandscapeTheme for Chrome and Iron The Prospector – Home Dash Extension Creates a Whole New Browsing Experience in Firefox KinEmote Links Kinect to Windows Why Nobody Reads Web Site Privacy Policies [Infographic] Asian Temple in the Snow Wallpaper 10 Weird Gaming Records from the Guinness Book

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• XQuery fn:replace not behaving as expected

  - by CoolGravatar

  I have an Excel worksheet in XML format which contains <Cell ss:StyleID="s127"><Data ss:Type="String">A01-Replace</Data></Cell> I want to replace @A01-Replace with a different string. I'm using the XQuery's replace function like so: let $excel := doc("excel.xml") let $test := "another string" return replace($excel, "(A[0-9]+-Replace)", $test) Before calling replace, the variable $excel is valid XML upon output. However, when I output $excel after I call the replace function, all of the XML tags have been stripped, and $excel is a string with the content of the cells as its values. I would like to keep the XML tags there. Any ideas?

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• Internal mic not working on Aspire One D255

  - by user50652

  I can't get my internal mic to work with any app other than Sound Recorder. I've scoured the other posts on this topic and none seem to have an answer. I've installed Alsa Mixer, Pulse Audio controls, tried minimising one of the stereo channels but nothing works. The mic is not muted. There is no function key on the keyboard to mute the mic either. The only connector options are analogue mic or analgue input. Neither do anything.

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• "Anagram solver" based on statistics rather than a dictionary/table?

  - by James M.

  My problem is conceptually similar to solving anagrams, except I can't just use a dictionary lookup. I am trying to find plausible words rather than real words. I have created an N-gram model (for now, N=2) based on the letters in a bunch of text. Now, given a random sequence of letters, I would like to permute them into the most likely sequence according to the transition probabilities. I thought I would need the Viterbi algorithm when I started this, but as I look deeper, the Viterbi algorithm optimizes a sequence of hidden random variables based on the observed output. I am trying to optimize the output sequence. Is there a well-known algorithm for this that I can read about? Or am I on the right track with Viterbi and I'm just not seeing how to apply it?

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• Problem with keyboard and trackpad on ubuntu 12.04

  - by Cdub

  Have a really strange issue with my keyboard and trackpad after installing ubuntu 12.04. It picked up both fine with the livecd and in the install, but for quite awhile now, I find when I power my laptop up (Toshiba Satellite L775D-S7132), when I hit the login screen much of the time I won't have any keyboard or touchpad. I can plug in a usb mouse and then at least restart or shut the laptop down and then keep trying until it picks it up correctly, but it's really a pain to have to do that all the time. Are there quite a few bugs related to keyboard and trackpad issues with the new version? I really want to get this issue resolved as it's a major nuisance. Otherwise, my hardware gets picked up fine. Video, audio, wlan, usb work perfectly and I don't ever have any issues with them. What's the best way to figure out the problem? Thanks in advance, C.

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• How to know file type without extension

  - by Ayusman

  While trying to come-up with a servlet based application to read files and manipulate them (image type conversion) here is a question that came up to me: Is it possible to inspect a file content and know the filetype? Is there a standard that specifies that each file MUST provide some type of marker in their content so that the application will not have to rely on the file extension constraints? Consider an application scenario: I am creating an application that will be able to convert different file formats to a set of output formats. Say user uploads an PDF, my application can suggest that the possible conversion formats are microsoft word or TIFF or JPEG etc. As my application will gradually support different file formats (over a period of time), I want my application to inspect the input file instead of having the user to specify the format. And suggest to user the possible formats of output. I understand this is an open ended, broad question. Please let me know if it needs to be modified. Thanks, Ayusman

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• Determine if PowerShell function is running as part of a pipeline?

  - by Richard Cook

  Can a PowerShell function determine if it is being run as part of a pipeline? I have a function which populates an array with instances of FileInfo which I would like to "yield" to the pipeline if the function is being run this way or produce some pretty output if the function is being invoked by itself from the command line. function Do-Something { $file_infos = @() # Populate $file_infos with FileInfo instances... if (INVOKED_IN_PIPELINE) { return $file_infos } else { foreach ($file_info in $file_infos) { write-host -foregroundcolor yellow $file_info.fullname } } } Basically, I'm trying to figure out how to implement INVOKED_IN_PIPELINE. If it is run in a pipeline (e.g. Do-Something | format-table fullname), I would simply yield the array, but if run directly (e.g. Do-Something), it would simply pretty-print the output. Is there a way to do this? If there is a more "idiomatic" way to achieve this kind of thing, I would also be interested to know.

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• Calling Graphviz dot from Java

  - by garsh0p

  What's the best way to call an external program (graphviz's dot in this case) from a Java program and grab the output?

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• How to reduce noise in Skype?

  - by tkc

  According to Alsamixer I do have a HDA Intel soundcard with Nvidia MCP77/78 HDMI chip (Realtek sound card on MSI notebook). When I use Skype under Ubuntu 12.04 for video calls, the other side hears background noise such as in Windows when you have your microphone boosted. In fact they can hear everything, even the fans turning on. There is nothing tweaked on Ubuntu's fresh installation. Also tried this site: https://code.launchpad.net/~ubuntu-audio-dev/+archive/alsa-daily/+packages , but there are no *.deb files that I can test if any fix the problem. The question is if there is a way to add/tweak something to enable on software level the noise cancellation like the Windows sound drivers have that option. I use my build in mic.

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• Check my anagram code from a job interview in the past.

  - by Michael Dorgan

  Had the following as an interview question a while ago and choked so bad on basic syntax that I failed to advance (once the adrenalin kicks in, coding goes out the window.) Given a list of string, return a list of sets of strings that are anagrams of the input set. i.e. "dog","god", "foo" should return {"dog","god"}. Afterward, I created the code on my own as a sanity check and it's been around now for a bit. I'd welcome input on it to see if I missed anything or if I could have done it much more efficiently. Take it as a chance to improve myself and learn other techniques: void Anagram::doWork(list input, list &output) { typedef list SortType; SortType sortedInput; // sort each string and pair it with the original for(list<string>::iterator i = input.begin(); i != input.end(); ++i) { string tempString(*i); std::sort(tempString.begin(), tempString.end()); sortedInput.push_back(make_pair(*i, tempString)); } // Now step through the new sorted list for(SortType::iterator i = sortedInput.begin(); i != sortedInput.end();) { set<string> newSet; // Assume (hope) we have a match and pre-add the first. newSet.insert(i->first); // Set the secondary iterator one past the outside to prevent // matching the original SortType::iterator j = i; ++j; while(j != sortedInput.end()) { if(i->second == j->second) { // If the string matches, add it to the set and remove it // so that future searches need not worry about it newSet.insert(j->first); j = sortedInput.erase(j); } else { // else, next element ++j; } } // If size is bigger than our original push, we have a match - save it to the output if(newSet.size() > 1) { output.push_back(newSet); } // erase this element and update the iterator i = sortedInput.erase(i); } }

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