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• Converting FASTQ to FASTA with SED/AWK

  - by neversaint

  I have a data in that always comes in block of four in the following format (called FASTQ): @SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN +SRR018006.2016 GA2:6:1:20:650 length=36 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+! @SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +SRR018006.19405469 GA2:6:100:1793:611 length=36 7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/ Is there a simple sed/awk/bash way to convert them into this format (called FASTA): >SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN >SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC In principle we want to extract the first two lines in each block-of-4 and replace @ with >.

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• Best way to handle multiple getView calls from inside an Adapter

  - by Samuh

  I have a ListView with custom ArrayAdapter. Each of the row in this ListView has an icon and some text. These icons are downloaded in background,cached and then using a callback, substituted in their respective ImageViews. The logic to get a thumbnail from cache or download is triggered every time getView() runs. Now, according to Romain Guy: "there is absolutely no guarantee on the order in which getView() will be called nor how many times." I have seen this happen, for a row of size two getView() was being called six times! How do I change my code to avoid duplicate thumbnail-fetch-requests and also handle view recycling? Thanks.

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• MySQL optimized sentence

  - by Ivan

  I have a simple table where I have to extract some records. The problem is that the evaluation function is a very time-consuming stored procedure so I shouldn't to call it twice like in this sentence: SELECT *, slow_sp(row) FROM table WHERE slow_sp(row)>0 ORDER BY dist DESC LIMIT 10 First I thought in optimize like this: SELECT *, slow_sp(row) AS value FROM table WHERE value>0 ORDER BY dist DESC LIMIT 10 But it doesn't works due "value" is not processed when the WHERE clause is evaluated. Any idea to optimize this sentence? Thanks.

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• "tailing" a binary file based on string location using bash?

  - by ilitirit

  I've got a bunch of binary files, each containing an embedded string near the end of the file but at different places (only occurs once in each file). I need to extract the part of the file starting at the location of the string till the end of the file and dump it into a new file. eg. If the file's contents is "AWREDEDEDEXXXERESSDSDS" and the string of interest is "XXX", then the part of the file I need is "XXXERESSDSDS". What's the easiest way to do this in bash?

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• Programmatically get screenshot of page

  - by Ender

  I'm writing a specialized crawler and parser for internal use and I require the ability to take a screenshot of a web page in order to check what colours are being used throughout. The program will take in around ten web addresses and will save them as a bitmap image, from there I plan to use LockBits in order to create a list of the five most used colours within the image. To my knowledge it's the easiest way to get the colours used within a web page but if there is an easier way to do it please chime in with your suggestions. Anyway, I was going to use this program until I saw the price tag. I'm also fairly new to C#, having only used it for a few months. Can anyone provide me with a solution to my problem of taking a screenshot of a web page in order to extract the colour scheme?

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• Obfuscating Geocode results to protect privacy?

  - by Kevin

  I have an app that finds other users within a 20 mile radius on a google map and associates an icon with each of them. However, I do not want their exact points to be given but rather an approximation. I've wrestled with a few ideas on how to do this: Only Geocode the Zip Code, make graphic icons for 1-99, use the icon to represent how many results are within the zip code, and use the info window to show hyperlinks to the individual results. The only problem is, I'd like each individual icon to be shown because it just looks a lot better. Add/Subtract a random number to the lat/lng values stored with each user and add a translucent circle around the icon. What do you guys suggest?

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• How to parse the MailMessage object from raw email string

  - by Xmindz

  I have written a program in C# which connects to a POP Server and retrieves raw email message strings from the server using POP3 command RETR. Since the email message being retrieved by the program is in plain text format with all the headers and message body with in the same, its too difficult to extract each header and mail body from the raw string. Could anybody tell me a solution by which I can parse the entire raw text to a System.Net.Mail.MailMessage object? Following is a sample email raw string: +OK 1281 octets Return-Path: <[email protected]> Delivered-To: samplenet-sample:[email protected] X-Envelope-To: [email protected] Received: (qmail 53856 invoked from network); 22 Sep 2012 06:11:46 -0000 Received: from mailwash18.pair.com (66.39.2.18) MIME-Version: 1.0 From: "Deepu" <[email protected]> To: [email protected] Date: 22 Sep 2012 11:41:39 +0530 Subject: TEST Subject Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Message-Id: <[email protected]> TEST Body .

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• Nonstandard SSIS lookup

  - by Stefan

  I have a situation where I am trying to lookup a value in one table based on values in another table, using a BETWEEN operator and not an = operator. In one table, I have a value "EffectiveDate". I want to get a Weight number from another table, but the other table has two fields: "Inception" and "Termination". What I want to do is extract the Weight from that table for use where the EffectiveDate is between Inception and Termination. SSIS doesn't seem to provide a way to do this. It's good at matching one column to another column, but doesn't seem to allow one to many-column comparison/operations. Am I missing anything? Is this possible to do somehow?

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• Is there a way to extracting semantic informations from PDF? (converting PDF to pure XHTML)

  - by Eonil

  Hi. I'm finding a way to extract semantic structural informations (like title, heading, paragraph or lists) from PDF. Because I want to get a pure structural data from PDF. Finally, I want to create an pure XHTML from the PDF. With only structural informations. No design or layout. I know, PDF can be created without any structural information. I don't consider those PDFs. Only regularly well-structured PDFs are considered. I'm new to PDF. So I don't know it offers regular semantic structure or not. If it exists, it's library will offer it. So I want to know whether PDF spec has those information, and best way to get those information if exists.

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• Any Java library for address extraction from emails?

  - by Hans Klock

  I'm looking for an Java open-source library which is able to extract address information from a (German) email (signature). The library should find name street city, city code/postal code email tel/fax address-parser.com is an commercial product, but a free (albeit simple) library would be great. stackoverflow.com/questions/16413/parse-usable-street-address-city-state-zip-from-a-string is asking for something similar, but my problem is broader because the address information is hidden in a complete email. And there isn't a solution either... Any ideas?

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• Using a UIPickerView to make a CoreData Relationship

  - by DVG

  Okay, so I have a fairly simple application set up. I have two different CoreData Entities, Games and Platforms, each have one attribute: name, and they have a one-to-many relationship between them. Platforms are populated on the first launch of the application, and will never change as a result of user input. I'm working on my Add view to let the user add new games to their personal database, and each game should select from a platform. The add view itself is a grouped table view with static custom cells. Tapping the platform cell should advance the user to another view to select the platform. My thought is that UIPickerView seems like a logical choice for the control, since the Platform list is static, but I'm not sure how to use it with CoreData. Even if I construct a fetch request to get the Platform objects and extract the strings out, how do I go about linking the new Game object to the original Platform object?

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• Can I embed an icon to a .hta file?

  - by BoltBait

  I have written an HTML Application (hta file) and am wondering if there is a way to embed an icon file into the hta file itself. I have seen html emails that include embedded graphic files, is there any way to do this with html applications and icons? HTA files have an HTA:APPLICATION tag that allows you to specify an icon, but I want to have only a single file for download. I don't want to have an external icon file. Is this possible? More info on hta files here: HTA files.

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• Php using unserialize() and serialize() changing values in a saved file

  - by Doodle

  I have a serialized array of values saved to a file and need to change the value of one of the variables. In the example I change the value of $two and then save the whole array back into the file with the new value. Is there a more efficient way of altering just the single value with out having to read and write the entire file/array. $data = file_get_contents('./userInfo'); $data = unserialize($data); extract($data); $two="this is a altered value"; $userData = array( 'one' => $one, 'two' => $two, 'three' => $three ); $file=fopen("../userInfo",'w'); fwrite($file, $userData); fclose($file);

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• c# library that extracts gmail,yahoomail and AOL contacts..

  - by Pandiya Chendur

  Is there any good c# library that extracts gmail,yahoomail and AOL contacts? Any suggestion... I looked at Opencontacts.net and i used opencontacts.dll in my asp.net web application but i can't able to make it work... It shows an error Could not load file or assembly 'Utilities, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. The system cannot find the file specified..... I did this, OpenContactsNet.GmailExtract gm = new OpenContactsNet.GmailExtract(); NetworkCredential nw =new NetworkCredential("[email protected]","***"); OpenContactsNet.MailContactList ml = new OpenContactsNet.MailContactList(); gm.Extract(nw, out ml); I am in search of any other c# library which would do my needs....

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• Redirect and parse in realtime stdout of an long running process in vb.net

  - by Richard

  Hello there, This code executes "handbrakecli" (a command line application) and places the output into a string: Dim p As Process = New Process p.StartInfo.FileName = "handbrakecli" p.StartInfo.Arguments = "-i [source] -o [destination]" p.StartInfo.UseShellExecute = False p.StartInfo.RedirectStandardOutput = True p.Start Dim output As String = p.StandardOutput.ReadToEnd p.WaitForExit The problem is that this can take up to 20 minutes to complete during which nothing will be reported back to the user. Once it's completed, they'll see all the output from the application which includes progress details. Not very useful. Therefore I'm trying to find a sample that shows the best way to: Start an external application (hidden) Monitor its output periodically as it displays information about it's progress (so I can extract this and present a nice percentage bar to the user) Determine when the external application has finished (so I can't continue with my own applications execution) Kill the external application if necessary and detect when this has happened (so that if the user hits "cancel", I get take the appropriate steps) Does anyone have any recommended code snippets?

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• Greasemonkey: load url using GM_xmlhttpRequest and createContextualFragment

  - by Dave

  I have the following GreaseMonkey Script: GM_xmlhttpRequest({ method: 'GET', url: "http://www.testurl.com", headers: { 'User-agent': 'Mozilla/4.0 (compatible) Greasemonkey/0.3', }, onload: function(responseDetails) { var tagString = responseDetails.responseText; var range = document.createRange(); range.selectNode(document.body); var documentFragment = range.createContextualFragment(tagString); How do I now extract stuff from documentFragment? documentFragment.getElementById(''), document.body etc all returns undefined. I suspect this is due to the createContextualFragment method returning a XPCNativeWrapper object, but how do I work around this to access the underlying DOM? Thanks

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• Entity Framework connection metadata extraction

  - by James

  Hi, I am using the EntityFramework POCO adapter and since there are limitations to what microsoft gives access to with regards to the meta data, i am manually extracting the information i need out of the xml. The only problem is i want to get the ssdl, msl, csdl file names to load without having to directly check for the connection string node in app.config. In short where in the ObjectContext/EntityConnection can i get access to these file names? Worst case scenario i need to get the connection name from the EntityConnection object then load this from app.config and parse the string itself and extract the filenames myself. (But i obviously don't want to do that). Thanks

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• iPhone facebook connect FQL Query to get Profile URL.

  - by user306641

  Hai. I am using Face book Connect FQL Queries to extract my profile photo url that is src_big,src_small URL. But i am always getting the empty array in below delegate (void)request:(FBRequest*)request didLoad:(id)result My FQL query is. NSString* fql = [NSString stringWithFormat:@"SELECT src_big,src_small FROM photo WHERE pid IN (SELECT cover_pid FROM album WHERE owner =%lld AND name ='Profile Pictures')", session.uid]; NSDictionary* params = [NSDictionary dictionaryWithObject:fql forKey:@"query"]; [[FBRequest requestWithDelegate:self] call:@"facebook.fql.query" params:params]; But - (void)request:(FBRequest*)request didLoad:(id)result always return the empty result. Can any one please correct me if there any mistake.

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• Refactoring a C# derived class with method dependancies

  - by drelihan

  Hi Folks, I want to get your opinion on this. I have a class which is derived from a base class. I don't have control over the code in the base class and it is critical to the system that I derive from it. In my class I inherite two methods that are critical to the system and are used in pretty much every function, many times. I intend to refactor this derived class and extract some classes from it - this won't be a problem. What I'm not sure about is, is it worth extracting class if I have to constantly make call backs to my main class to access the two methods (or public wrappers to the methods)??? Thanks

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• Screen scrape a web page that uses javaScript and frames

  - by Mello

  Hi, I want to scrape data from www.marktplaats.nl . I want to analyze the scraped description, price, date and views in Excel/Access. I tried to scrape data with Ruby (nokogiri, scrapi) but nothing worked. (on other sites it worked well) The main problem is that for example selectorgadget and the add-on firebug (Firefox) don’t find any css I can use to scrape the page. On other sites I can extract the css with selectorgadget or firebug and use it with nokogiri or scrapi. Due to lack of experience it is difficult to identify the problem and therefore searching for a solution isn’t easy. Can you tell me where to start solving this problem and where I maybe can find more info about a similar scraping process? Thanks in advance!

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• A CSS code to put text saved in other server into blogspot blog..???

  - by Nok Imchen

  I have a blog hosted on blogspot dot com. In that blog, i want to put some data like Google search string or etc automatically. I want it to be done in this way: Just put a code (server side scripting) linking to a text file or PHP file, and the code will extract the text and output in my blogspot blog. What i DONT want is to use javascript. Beacause, if i use javascript then the output will be seen only in the users screen. I want the output to be seen by Google Bot too. Thanking you in anticipation.

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• using Dependency Parser in Stanford coreNLP

  - by Eddie Dovzhik

  I am using the Stanford coreNLP ( http://nlp.stanford.edu/software/corenlp.shtml ) in order to parse sentences and extract dependencies between the words. I have managed to create the dependencies graph like in the example in the supplied link, but I don't know how to work with it. I can print the entire graph using the toString() method, but the problem I have is that the methods that search for certain words in the graph, such as getChildList, require an IndexedWord object as a parameter. Now, it is clear why they do because the nodes of the graph are of IndexedWord type, but it's not clear to me how I create such an object in order to search for a specific node. For example: I want to find the children of the node that represents the word "problem" in my sentence. How I create an IndexWord object that represents the word "problem" so I can search for it in the graph?

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• deploying gwt web application on jetty

  - by Azhar

  Hi I am deploying my web application created in Gwt on the jetty. I have used mongodb as my database.After starting the server it starts deploying the weapp.war and gives following error - 694 [main] INFO org.mortbay.log - Extract /usr/share/jetty/webapps/myapp.war to /tmp/Jetty_0_0_0_0_8090_myapp.war__myapp__n6yltk/webapp 3567 [main] WARN org.mortbay.log - failed Startup: java.lang.LinkageError: loader constraint violation: loader (instance of org/mortbay/jetty/webapp/WebAppClassLoader) previously initiated loading for a different type with name "javax/management/MBeanServer" at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:634) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at org.mortbay.jetty.webapp.WebAppClassLoader.loadClass(WebAppClassLoader.java:392) at org.mortbay.jetty.webapp.WebAppClassLoader.loadClass(WebAppClassLoader.java:363) at com.mongodb.DBPortPool$Holder.get(DBPortPool.java:58) at com.mongodb.DBTCPConnector._set(DBTCPConnector.java:458) at com.mongodb.DBTCPConnector.<init>(DBTCPConnector.java:46) at com.mongodb.Mongo.<init>(Mongo.java:137) at com.mongodb.Mongo.<init>(Mongo.java:123)

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• Visualizing read-only folders

  - by Paul-Jan

  My application displays a folder structure in a tree. The user can browse the contents in these folders, and drag content into the folders. However, some of these folders are readonly (meaning no content can be dragged into them). I'm looking for a clear way of depicting this to the user, so they are aware which folders they can drag to before actually having to try it, i.e. hover state. Something not too alarming or interrupting (no big red crosses overlayed on top of the folder icons, for instance), preferably a recognized standard. Specifically, we are talking about an Outlook add-in showing a SharePoint folder tree here, but I'd much rather get the answer from a generic viewpoint. From the top of my head, I simply don't seem to know any applications that visually mark readonly folders.

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• Spring @Autowired and WebApplicationContext in Tomcat

  - by EugeneP

  @Autowired works only once. What to do to make it wire the bean every time the Servlet is recreated? My web-app (Tomcat6 container) consists of 2 Servlets. Every servlet has private fields. Their setters are marked with @Autowired In the init method I use WebApplicationContextUtils ... autowireBean(this); It autowires the properties marked with @Autowired once - during the initialization of the Servlet. Any other session will see these fields values, they will not be rewired after the previous session is destroyed. What to do to make them rewire them each time a Servlet constructor is called? a) Put the autowiring into the constructor? Or better 2) get a web app context and extract a bean from there?

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