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  • BioPython: extracting sequence IDs from a Blast output file

    - by Jon
    Hi, I have a BLAST output file in XML format. It is 22 query sequences with 50 hits reported from each sequence. And I want to extract all the 50x22 hits. This is the code I currently have, but it only extracts the 50 hits from the first query. from Bio.Blast import NCBIXM blast_records = NCBIXML.parse(result_handle) blast_record = blast_records.next() save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w') for alignment in blast_record.alignments: for hsp in alignment.hsps: save_file.write('>%s\n' % (alignment.title,)) save_file.close() Somebody have any suggestions as to extract all the hits? I guess I have to use something else than alignments. Hope this was clear. Thanks! Jon

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  • Transferring a flat file database to a MySQL database

    - by Jon
    I have a flat file database (yeah gross I know - the worst part is that it's 1.4GB), and I'm in the process of moving it to a MySQL database. The problem is that I'm not sure how to go about doing this - and I've checked through every related question on here but none relate to what I want to do, nor how my database is currently setup. My current flat file database is setup to where a normal MySQL row is its own file, and a MySQL table would be the directory. So for example if you have a user named Jon, there would be a file for the user in a directory named /members/. Within that file would be various information for the user including the users id, rank etc - all separated by tabs, all on separate lines (userid\t4). So here's an example user file: userid 4 notes staff notes: bla bla staff2 notes: bla bla bla username Example So how can I convert the above into their own rows and fields in MySQL? And if possible, could I do thousands of these files at once? Thanks.

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  • NHibernate HQL logic problem

    - by Jon
    Hi I'm trying to write an NHibernate HQL query that makes use of parenthesis in the where clause. However, the HQL parser seems to be ignoring my parenthesis, thus changing the meaning of my statement. Can anyone shed any light on the matter? The following HQL query: from WebUser u left join fetch u.WebUserProfile left join fetch u.CommunicationPreferences where (u.CommunicationPreferences.Email = 0 and u.SyncDate is not null) or u.DateDeleted is not null translates to: from WebUser webuser0_ left outer join WebUserProfile webuserpro1_ on webuser0_.UserId = webuserpro1_.WebUserId left outer join WebUserCommunicationPreferences communicat2_ on webuser0_.UserId = communicat2_.UserId where communicat2_.Email = 0 and (webuser0_.SyncDate is not null) or webuser0_.DateDeleted is not null Thanks Jon

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  • Is there a good AddIn for Visual Studio that will launch msbuild targets?

    - by Jon Lent
    One of the things I like about the Java IDEs out there is that they typically have the ability to allow a user to right-click on an Ant file and run one of the targets. I've got an msbuild file in my solution that is used for migrating the application database, and would kill to be able to right-click on it, select "update" or "rollback" and have it run. My searching has not turned up anything meant to run inside VS2008, just a shell extension for windows explorer. Has anybody seen such an animal out there? Cordially, Jon

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  • bash command history update before execution of command

    - by Jon
    Hi, Bash's command history is great, especially it is useful when adding the history -a command to the COMMAND_PROMPT. However, I'm wondering if there is a way to log the commands to a file as soon as the Return key is pressed, e.g. before starting the command and not on completion of the command (using the COMMAND_PROMPT option would save the command once the prompt is there again). I read about auditing programs like snoopy and session recorder like script but I thought they're already too complex for the simple question I have. I guess that deactivating that script logs all the output of the command would lead already in the right direction but isn't there a quicker way to solve that probelm? Thanks, Jon

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  • Redirecting input to another view

    - by Jon
    My application is working fine on the normal iPad display, but I also need to output to VGA out. When I do this, I need to add the view to the external screen's window which seems to mean that I can't use it to accept input from the iPad screen. I want to redirect input from the iPad's window to the window displaying on the external screen. As far as I can tell there's no standard method of doing this. I've tried overriding hitTest on the iPad's window view to send it to the window on the external display, but the coordinates seem to get messed up in the process which makes it nigh unusable. I've also tried subclassing the iPad's UIWindow and catching events in sendEvent, then trying to send them to the external window, but this doesn't seem to work at all. Any help would be appreciated, I'm happy to post any code you would like to see. Thanks, Jon

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  • How to draw a line of plusses og triangles along a path in WPF?

    - by Jon H
    I need to draw a line with plusses or crosses along an given path (arch) but can't seem to find anything pointing me in the right direction. Any help would me much appreciated. Best, Jon H Edit: Hmmm. I still cant find any good answer to my question. I have googled for "everything"...I have fooled around with DrawingBrush'es with various LineGeometries or GeometryDrawings but cant seem to get a hang on it. Am I on the right coures or is there a better way? Can this be done in Blend/Design and exported in some way?

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  • What's the best name for a non-mutating "add" method on an immutable collection?

    - by Jon Skeet
    Sorry for the waffly title - if I could come up with a concise title, I wouldn't have to ask the question. Suppose I have an immutable list type. It has an operation Foo(x) which returns a new immutable list with the specified argument as an extra element at the end. So to build up a list of strings with values "Hello", "immutable", "world" you could write: var empty = new ImmutableList<string>(); var list1 = empty.Foo("Hello"); var list2 = list1.Foo("immutable"); var list3 = list2.Foo("word"); (This is C# code, and I'm most interested in a C# suggestion if you feel the language is important. It's not fundamentally a language question, but the idioms of the language may be important.) The important thing is that the existing lists are not altered by Foo - so empty.Count would still return 0. Another (more idiomatic) way of getting to the end result would be: var list = new ImmutableList<string>().Foo("Hello"); .Foo("immutable"); .Foo("word"); My question is: what's the best name for Foo? EDIT 3: As I reveal later on, the name of the type might not actually be ImmutableList<T>, which makes the position clear. Imagine instead that it's TestSuite and that it's immutable because the whole of the framework it's a part of is immutable... (End of edit 3) Options I've come up with so far: Add: common in .NET, but implies mutation of the original list Cons: I believe this is the normal name in functional languages, but meaningless to those without experience in such languages Plus: my favourite so far, it doesn't imply mutation to me. Apparently this is also used in Haskell but with slightly different expectations (a Haskell programmer might expect it to add two lists together rather than adding a single value to the other list). With: consistent with some other immutable conventions, but doesn't have quite the same "additionness" to it IMO. And: not very descriptive. Operator overload for + : I really don't like this much; I generally think operators should only be applied to lower level types. I'm willing to be persuaded though! The criteria I'm using for choosing are: Gives the correct impression of the result of the method call (i.e. that it's the original list with an extra element) Makes it as clear as possible that it doesn't mutate the existing list Sounds reasonable when chained together as in the second example above Please ask for more details if I'm not making myself clear enough... EDIT 1: Here's my reasoning for preferring Plus to Add. Consider these two lines of code: list.Add(foo); list.Plus(foo); In my view (and this is a personal thing) the latter is clearly buggy - it's like writing "x + 5;" as a statement on its own. The first line looks like it's okay, until you remember that it's immutable. In fact, the way that the plus operator on its own doesn't mutate its operands is another reason why Plus is my favourite. Without the slight ickiness of operator overloading, it still gives the same connotations, which include (for me) not mutating the operands (or method target in this case). EDIT 2: Reasons for not liking Add. Various answers are effectively: "Go with Add. That's what DateTime does, and String has Replace methods etc which don't make the immutability obvious." I agree - there's precedence here. However, I've seen plenty of people call DateTime.Add or String.Replace and expect mutation. There are loads of newsgroup questions (and probably SO ones if I dig around) which are answered by "You're ignoring the return value of String.Replace; strings are immutable, a new string gets returned." Now, I should reveal a subtlety to the question - the type might not actually be an immutable list, but a different immutable type. In particular, I'm working on a benchmarking framework where you add tests to a suite, and that creates a new suite. It might be obvious that: var list = new ImmutableList<string>(); list.Add("foo"); isn't going to accomplish anything, but it becomes a lot murkier when you change it to: var suite = new TestSuite<string, int>(); suite.Add(x => x.Length); That looks like it should be okay. Whereas this, to me, makes the mistake clearer: var suite = new TestSuite<string, int>(); suite.Plus(x => x.Length); That's just begging to be: var suite = new TestSuite<string, int>().Plus(x => x.Length); Ideally, I would like my users not to have to be told that the test suite is immutable. I want them to fall into the pit of success. This may not be possible, but I'd like to try. I apologise for over-simplifying the original question by talking only about an immutable list type. Not all collections are quite as self-descriptive as ImmutableList<T> :)

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  • Trying to use Digest Authentication for Folder Protection

    - by Jon Hazlett
    StackOverflow users suggested I try my question here. I'm using Server 2008 EE and IIS 7. I've got a site that I've migrated over from XP Pro using IIS 5. On the old system, I was using IIS Password to use simple .htaccess files to control a couple of folders that I didn't want to be publicly viewable. Now that I'm running a full-blown DC with a more powerful version of IIS, I decided it'd be a good idea to start using something slightly more sophisticated. After doing my research and trying to keep things as cheap as possible with a touch of extra security, I decided that Digest Authentication would be the best way to go. My issue is this: With Anon access disabled and Digest enabled, I am never prompted for credentials. when on the server, viewing domain[dot]com/example will simply show my 401.htm page without prompting me for credentials. when on a different network/computer, viewing domain[dot]com/example again shows my 401.htm without prompting for credentials. At the site level I only have Anon enabled. Every subfolder, unless I want it protected, has just Anon enabled. Only the folders I want protected have Anon disabled and Digest enabled. I have tried editing the bindings to see if that would spark any kind of change... www.domain.com, domain.com, and localhost have all been tried. There was never a change in behavior at any permutation (aside from the page not being found when I un-bound localhost to the site). I might have screwed up when I deleted the default site from IIS. I didn't think I'd actually need it for anything, but some of what I have read online is telling me otherwise now. As for Digest settings, I have it pointed to local.domain.com, which is the name assigned to my AD Domain. I'm guessing that's right, but honestly have no clue about what a realm actually is. Would it matter that I have an A record for local.domain.com pointing to my IP address? I had problems initially with an absolute link for 401.htm pages, but have since resolved that. Instead of D:\HTTP\401.htm I've used /401.htm and all is well. I used to get error 500's because it couldn't find the custom 401.htm file, but now it loads just fine. As for some data, I was getting entries like this from access logs: 2009-07-10 17:34:12 10.0.0.10 GET /example/ - 80 - [workip] Mozilla/4.0+(compatible;+MSIE+7.0;+Windows+NT+5.1;+.NET+CLR+1.1.4322;+.NET+CLR+2.0.50727;+InfoPath.2) 401 2 5 132 But after correcting my 401.htm links now get logs like this: 2009-07-10 18:56:25 10.0.0.10 GET /example - 80 - [workip] Mozilla/5.0+(Windows;+U;+Windows+NT+5.1;+en-US;+rv:1.9.0.11)+Gecko/2009060215+Firefox/3.0.11 200 0 0 146 I don't know if that means anything or not. I still don't get any credential challenges, regardless of where I try to sign in from ( my workstation, my server, my cellphone even ). The only thing that's seemed to work is viewing localhost and I donno what could be preventing authentication from finding it's way out of the server. Thanks for any help! Jon

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  • What's the strangest corner case you've seen in C# or .NET?

    - by Jon Skeet
    I collect a few corner cases and brain teasers and would always like to hear more. The page only really covers C# language bits and bobs, but I also find core .NET things interesting too. For example, here's one which isn't on the page, but which I find incredible: string x = new string(new char[0]); string y = new string(new char[0]); Console.WriteLine(object.ReferenceEquals(x, y)); I'd expect that to print False - after all, "new" (with a reference type) always creates a new object, doesn't it? The specs for both C# and the CLI indicate that it should. Well, not in this particular case. It prints True, and has done on every version of the framework I've tested it with. (I haven't tried it on Mono, admittedly...) Just to be clear, this is only an example of the kind of thing I'm looking for - I wasn't particularly looking for discussion/explanation of this oddity. (It's not the same as normal string interning; in particular, string interning doesn't normally happen when a constructor is called.) I was really asking for similar odd behaviour. Any other gems lurking out there?

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  • Performance surprise with "as" and nullable types

    - by Jon Skeet
    I'm just revising chapter 4 of C# in Depth which deals with nullable types, and I'm adding a section about using the "as" operator, which allows you to write: object o = ...; int? x = o as int?; if (x.HasValue) { ... // Use x.Value in here } I thought this was really neat, and that it could improve performance over the C# 1 equivalent, using "is" followed by a cast - after all, this way we only need to ask for dynamic type checking once, and then a simple value check. This appears not to be the case, however. I've included a sample test app below, which basically sums all the integers within an object array - but the array contains a lot of null references and string references as well as boxed integers. The benchmark measures the code you'd have to use in C# 1, the code using the "as" operator, and just for kicks a LINQ solution. To my astonishment, the C# 1 code is 20 times faster in this case - and even the LINQ code (which I'd have expected to be slower, given the iterators involved) beats the "as" code. Is the .NET implementation of isinst for nullable types just really slow? Is it the additional unbox.any that causes the problem? Is there another explanation for this? At the moment it feels like I'm going to have to include a warning against using this in performance sensitive situations... Results: Cast: 10000000 : 121 As: 10000000 : 2211 LINQ: 10000000 : 2143 Code: using System; using System.Diagnostics; using System.Linq; class Test { const int Size = 30000000; static void Main() { object[] values = new object[Size]; for (int i = 0; i < Size - 2; i += 3) { values[i] = null; values[i+1] = ""; values[i+2] = 1; } FindSumWithCast(values); FindSumWithAs(values); FindSumWithLinq(values); } static void FindSumWithCast(object[] values) { Stopwatch sw = Stopwatch.StartNew(); int sum = 0; foreach (object o in values) { if (o is int) { int x = (int) o; sum += x; } } sw.Stop(); Console.WriteLine("Cast: {0} : {1}", sum, (long) sw.ElapsedMilliseconds); } static void FindSumWithAs(object[] values) { Stopwatch sw = Stopwatch.StartNew(); int sum = 0; foreach (object o in values) { int? x = o as int?; if (x.HasValue) { sum += x.Value; } } sw.Stop(); Console.WriteLine("As: {0} : {1}", sum, (long) sw.ElapsedMilliseconds); } static void FindSumWithLinq(object[] values) { Stopwatch sw = Stopwatch.StartNew(); int sum = values.OfType<int>().Sum(); sw.Stop(); Console.WriteLine("LINQ: {0} : {1}", sum, (long) sw.ElapsedMilliseconds); } }

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  • What's your most controversial programming opinion?

    - by Jon Skeet
    This is definitely subjective, but I'd like to try to avoid it becoming argumentative. I think it could be an interesting question if people treat it appropriately. The idea for this question came from the comment thread from my answer to the "What are five things you hate about your favorite language?" question. I contended that classes in C# should be sealed by default - I won't put my reasoning in the question, but I might write a fuller explanation as an answer to this question. I was surprised at the heat of the discussion in the comments (25 comments currently). So, what contentious opinions do you hold? I'd rather avoid the kind of thing which ends up being pretty religious with relatively little basis (e.g. brace placing) but examples might include things like "unit testing isn't actually terribly helpful" or "public fields are okay really". The important thing (to me, anyway) is that you've got reasons behind your opinions. Please present your opinion and reasoning - I would encourage people to vote for opinions which are well-argued and interesting, whether or not you happen to agree with them.

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  • What does the following FORTRAN code do?

    - by Jon Skeet
    C AREA OF A TRIANGLE WITH A STANDARD SQUARE ROOT FUNCTION C INPUT - CARD READER UNIT 5, INTEGER INPUT C OUTPUT - LINE PRINTER UNIT 6, REAL OUTPUT C INPUT ERROR DISPLAY ERROR OUTPUT CODE 1 IN JOB CONTROL LISTING READ (5, 501) IA, IB, IC 501 FORMAT (3I5) C IA, IB, AND IC MAY NOT BE NEGATIVE C FURTHERMORE, THE SUM OF TWO SIDES OF A TRIANGLE C IS GREATER THAN THE THIRD SIDE, SO WE CHECK FOR THAT, TOO IF (IA) 777, 777, 701 701 IF (IB) 777, 777, 702 702 IF (IC) 777, 777, 703 703 IF (IA+IB-IC) 777,777,704 704 IF (IA+IC-IB) 777,777,705 705 IF (IB+IC-IA) 777,777,799 777 STOP 1 C USING HERON'S FORMULA WE CALCULATE THE C AREA OF THE TRIANGLE 799 S = FLOATF (IA + IB + IC) / 2.0 AREA = SQRT( S * (S - FLOATF(IA)) * (S - FLOATF(IB)) * + (S - FLOATF(IC))) WRITE (6, 601) IA, IB, IC, AREA 601 FORMAT (4H A= ,I5,5H B= ,I5,5H C= ,I5,8H AREA= ,F10.2, + 13H SQUARE UNITS) STOP END plz i need to know soon!!!!!

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  • c# convert file from one format to another

    - by JOE SKEET
    i have a bunch of files that need to be converted. the beginning files look like this: Well ID,Error code,Sample Barcode A1,0,THC_CAL1 B1,0,THC_CAL2 C1,1,THC_CAL3 D1,0,THC_CAL4 E1,0,THC_QC1 F1,0,THC_QC2 G1,0,THC_QC3 H1,0,THC_QC4 A2,0,BLANK0609 B2,0,AA178121 C2,0,CC37815 D2,0,BLANK0610 E2,0,CC37819 F2,0,N150680 G2,0,BLANK0611 H2,0,AA127900 A3,0,AA26940 B3,0,BLANK0612 ........... the output needs to look like this: A01 THC_CAL1 B01 THC_CAL2 D01 THC_CAL4 //please note that c1 is gone since it did not have a 0 in the middle column E01 THC_QC1 F01 THC_QC2 G01 THC_QC3 H01 THC_QC4 A02 BLANK0609 B02 AA178121 C02 CC37815 D02 BLANK0610 E02 CC37819 F02 N150680 G02 BLANK0611 H02 AA127900 A03 AA26940 B03 BLANK0612 H10 BLANK0234 //please notice that there is H10 and not H010 what would be the best way to read this file into a variable and then output this into a new file? should i read it line by line or should i read it into a datatable?

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  • So, whats the best book on C#?

    - by mbcrump
    I see this question several times a day from newbie’s to professionals. I have listed the best C# books that I have read so far.   ECMA-334 C# Language Specification. – FREE book. This is probably the best place to start. Read it backwards and forwards and you can even request a hard copy. Absolute Beginners Guide to C Sharp 2nd Edition – Used this early on and found it very useful even if its game programming. C-Sharp 2.0 - The Complete Reference, 2nd Edition (McGraw-Hill, 2006) – One of the most useful books that is always with me. It contains short example code and is very well written. Dot Net Zero - Charles Petzold  - FREE book and you should definately give it a read. C Sharp in Depth by Jon Skeet -  Probably one of the most in depth books on C Sharp and definitely not for beginners. Jon Skeet knows C# like no other. I would consider this book the Bible of C#. If you understand 50% of this book, you have a good understanding of the language.  CLR via C Sharp 3rd Edition – I just started reading this book and it is another book thats not for beginners. If you really want to understand the CLR then give this book a try. Well, thats it. I hope you enjoy the books as I have spent a lot of time researching different C# books.

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