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• Perl - string matching issue

  - by user2886545

  I have a problem I cannot understand. I have this string: gene_id "siRNA_Z27kG1_20543"transcript_id "siRNA_Z27kG1_20543_X_1";tss_id "TSS124620" And I want to change the gene_id. So, I have the following code: if ($line =~ /;transcript_id "([A-Za-z0-9:\-._]*)(_[oxOX][_.][0-9]*)";/) { $num = $2; $line =~ s/gene_id "([A-Za-z0-9:\-._]*)";/gene_id "$1$num";/g; print $new $line."\n"; } The aim of my code is to change siRNA_Z27kG1_20543 for siRNA_Z27kG1_20543_X_1. However, my code does not produce that output. Why? I can't understand that. My regex needs to be as it is because I match other strings (this time with success). Thanks.

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• Python Textwrap - forcing 'hard' breaks

  - by Tom Werner

  I am trying to use textwrap to format an import file that is quite particular in how it is formatted. Basically, it is as follows (line length shortened for simplicity): abcdef <- Ok line abcdef ghijk <- Note leading space to indicate wrapped line lm Now, I have got code to work as follows: wrapper = TextWrapper(width=80, subsequent_indent=' ', break_long_words=True, break_on_hyphens=False) for l in lines: wrapline=wrapper.wrap(l) This works nearly perfectly, however, the text wrapping code doesn't do a hard break at the 80 character mark, it tries to be smart and break on a space (at approx 20 chars in). I have got round this by replacing all spaces in the string list with a unique character (#), wrapping them and then removing the character, but surely there must be a cleaner way? N.B Any possible answers need to work on Python 2.4 - sorry!

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• sql server - bulk insert error

  - by user554134

  I am using bulk insert and getting below error: Note: The data in the load file is not beyong the configured column length Running Command: bulk insert load_data from 'C:\temp\dataload\load_file.txt' with (firstrow = 1, fieldterminator = '0x09', rowterminator = '\n',MAXERRORS = 0, ERRORFILE = 'C:\temp\dataload\load_file') Contents of load file: user_name file_path asset_owner city import_date admin C:\ admin toronto 04/12/2012 Error: Msg 4863, Level 16, State 1, Line 1 Bulk load data conversion error (truncation) for row 1, column 6 (validated). Msg 7399, Level 16, State 1, Line 1 The OLE DB provider "BULK" for linked server "(null)" reported an error. The provider did not give any information about the error. Msg 7330, Level 16, State 2, Line 1 Cannot fetch a row from OLE DB provider "BULK" for linked server "(null)".

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• CSV parser in C++

  - by User1

  All I need is a good CSV file parser for C++. At this point it can really just be a comma-delimited parser (ie don't worry about escaping new lines and commas). The main need is a line-by-line parser that will return a vector for the next line each time the method is called. I found this article which looks quite promising: http://www.boost.org/doc/libs/1_35_0/libs/spirit/example/fundamental/list_parser.cpp I've never used Boost's Spirit, but am willing to try it. Is it overkill/bloated or is it fast and efficient? Does anyone have faster algorithms using STL or anything else? Thanks!

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• MemoryError when running Numpy Meshgrid

  - by joaoc

  I have 8823 data points with x,y coordinates. I'm trying to follow the answer on how to get a scatter dataset to be represented as a heatmap but when I go through the X, Y = np.meshgrid(x, y) instruction with my data arrays I get MemoryError. I am new to numpy and matplotlib and am essentially trying to run this by adapting the examples I can find. Here's how I built my arrays from a file that has them stored: XY_File = open ('XY_Output.txt', 'r') XY = XY_File.readlines() XY_File.close() Xf=[] Yf=[] for line in XY: Xf.append(float(line.split('\t')[0])) Yf.append(float(line.split('\t')[1])) x=array(Xf) y=array(Yf) Is there a problem with my arrays? This same code worked when put into this example but I'm not too sure. Why am I getting this MemoryError and how can I fix this?

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• Is it stable to change I/O direction on microcontroller repeatedly?

  - by SS

  I'm new to microcontroller programming and I have interfaced my microcontroller board to another device that provides a status based on the command send to it but, this status is provided on the same I/O pin that is used to provide data. So basically, I have an 8-bit data line that is used as an output from the microcontroller, but for certain commands I get a status back on one of the data lines if I choose to read it. So I would be required to change the direction of this one line to read the status thus converting this line as an ouput to an input and then back to an output. Is this acceptable programming or will this changing of the I/O pin this frequently cause instability? Thanks.

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• Reloading Rails Directories on Change for Development, Not in Lib

  - by yar

  I have checked out several questions on this, including all of those you see next to the question. Unfortunately, I'm not working with a plugin, and I don't want to work in lib. I have a directory called File.join(Rails.root, 'classes') and I'd like the classes in this directory to reload automatically in dev. In my environment.rb I have this line config.load_paths << File.join(Rails.root, 'classes') which works fine and blows up if the path isn't there. The reloading line in my development.rb also works fine require_dependency File.join(Rails.root, 'classes', 'blah.rb') which blows up if the file is not there (a good sign). However, the file doesn't reload. This all works if the file is in the root of lib and I use the require_dependency line, but my whole point is to get stuff out of lib as suggested here.

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• Explain to me the following VS 2010 Extension Sample code..

  - by ealshabaan

  Coders, I am building a VS 2010 extension and I am experimenting around some of the samples that came with the VS 2010 SDK. One of the sample projects is called TextAdornment. In that project there is a weirdo class that looks like the following: [Export(typeof(IWpfTextViewCreationListener))] [ContentType("text")] [TextViewRole(PredefinedTextViewRoles.Document)] internal sealed class TextAdornment1Factory : IWpfTextViewCreationListener While I was experimenting with this project, I tried to debug the project to see the flow of the program and I noticed that this class gets hit when I first start the debugging. Now my question is the following: what makes this class being the first class to get called when VS starts? In other words, why this class gets active and it runs as of some code instantiate an object of this class type? Here is the only two files in the sample project: TextAdornment1Factory.cs using System.ComponentModel.Composition; using Microsoft.VisualStudio.Text.Editor; using Microsoft.VisualStudio.Utilities; namespace TextAdornment1 { #region Adornment Factory /// /// Establishes an to place the adornment on and exports the /// that instantiates the adornment on the event of a 's creation /// [Export(typeof(IWpfTextViewCreationListener))] [ContentType("text")] [TextViewRole(PredefinedTextViewRoles.Document)] internal sealed class TextAdornment1Factory : IWpfTextViewCreationListener { /// /// Defines the adornment layer for the adornment. This layer is ordered /// after the selection layer in the Z-order /// [Export(typeof(AdornmentLayerDefinition))] [Name("TextAdornment1")] [Order(After = PredefinedAdornmentLayers.Selection, Before = PredefinedAdornmentLayers.Text)] [TextViewRole(PredefinedTextViewRoles.Document)] public AdornmentLayerDefinition editorAdornmentLayer = null; /// <summary> /// Instantiates a TextAdornment1 manager when a textView is created. /// </summary> /// <param name="textView">The <see cref="IWpfTextView"/> upon which the adornment should be placed</param> public void TextViewCreated(IWpfTextView textView) { new TextAdornment1(textView); } } #endregion //Adornment Factory } TextAdornment1.cs using System.Windows; using System.Windows.Controls; using System.Windows.Media; using Microsoft.VisualStudio.Text; using Microsoft.VisualStudio.Text.Editor; using Microsoft.VisualStudio.Text.Formatting; namespace TextAdornment1 { /// ///TextAdornment1 places red boxes behind all the "A"s in the editor window /// public class TextAdornment1 { IAdornmentLayer _layer; IWpfTextView _view; Brush _brush; Pen _pen; ITextView textView; public TextAdornment1(IWpfTextView view) { _view = view; _layer = view.GetAdornmentLayer("TextAdornment1"); textView = view; //Listen to any event that changes the layout (text changes, scrolling, etc) _view.LayoutChanged += OnLayoutChanged; _view.Closed += new System.EventHandler(_view_Closed); //selectedText(); //Create the pen and brush to color the box behind the a's Brush brush = new SolidColorBrush(Color.FromArgb(0x20, 0x00, 0x00, 0xff)); brush.Freeze(); Brush penBrush = new SolidColorBrush(Colors.Red); penBrush.Freeze(); Pen pen = new Pen(penBrush, 0.5); pen.Freeze(); _brush = brush; _pen = pen; } void _view_Closed(object sender, System.EventArgs e) { MessageBox.Show(textView.Selection.IsEmpty.ToString()); } /// <summary> /// On layout change add the adornment to any reformatted lines /// </summary> private void OnLayoutChanged(object sender, TextViewLayoutChangedEventArgs e) { foreach (ITextViewLine line in e.NewOrReformattedLines) { this.CreateVisuals(line); } } private void selectedText() { } /// <summary> /// Within the given line add the scarlet box behind the a /// </summary> private void CreateVisuals(ITextViewLine line) { //grab a reference to the lines in the current TextView IWpfTextViewLineCollection textViewLines = _view.TextViewLines; int start = line.Start; int end = line.End; //Loop through each character, and place a box around any a for (int i = start; (i < end); ++i) { if (_view.TextSnapshot[i] == 'a') { SnapshotSpan span = new SnapshotSpan(_view.TextSnapshot, Span.FromBounds(i, i + 1)); Geometry g = textViewLines.GetMarkerGeometry(span); if (g != null) { GeometryDrawing drawing = new GeometryDrawing(_brush, _pen, g); drawing.Freeze(); DrawingImage drawingImage = new DrawingImage(drawing); drawingImage.Freeze(); Image image = new Image(); image.Source = drawingImage; //Align the image with the top of the bounds of the text geometry Canvas.SetLeft(image, g.Bounds.Left); Canvas.SetTop(image, g.Bounds.Top); _layer.AddAdornment(AdornmentPositioningBehavior.TextRelative, span, null, image, null); } } } } } }

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• php - Loop output in two diffrent divs?

  - by Stan

  I want to output my sql rows on each side of a line, without breaking the line. Forexample the html/css code i would like to end up with is something like this: <div id='container'> <div style='float:left;'> Even loops here.. </div> <div id='line' style='float:left;'> </div> <div style='float:right;'> Uneven loops here.. </div> <div style='clear:both;'></div> </div> Is there a way to output the sql rows in two diffrent divs?

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• how to set length and postion for repeat-x and scroll background-image?

  - by user550945

  Hi all, I have an to set background image. it is a red line under the input value. background-attachment:scroll; background-color:#FFFFFF; background-image:url("../images/errorLine.gif"); background-position:left bottom; background-repeat:repeat-x; the input value is like "123; 456; 789;". the red line cover all the string, its length is the same as the input width. Is there any way to make the red line only under the "456;"? Is there anyway to do it by CSS? Thanks a lot. Best regards, Ryanivanka

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• Deactivate any calls to Log before publishing: are there tools to do this?

  - by Nicolas Raoul

  According to Google, I must "Deactivate any calls to Log methods in the source code" before publishing my Android app (section 4 of the publication checklist). My open-source project is large and it is a pain to do it manually every time I release. Additionally, removing a Log line is potentially tricky, for instance: if(condition) Log.d(LOG_TAG, "Something"); data.load(); data.show(); If I comment the Log line, then the condition applies to the next line, and chances are load() is not called. Are such situations rare enough that I can decide it should exist? This is on the official checklist, so I guess many people do this on a regular basis. So, is there a tool that removes all Log lines? Preferably one that is not tricked by code like the above.

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• Accessing variablss through a different class within the constructor of latter classes of an object

  - by Haxed

  In the code below, I've added two lines that print output. The first line prints junk as usual, but surprisingly the second one gives me a compilation error. Why? class Student { private String name; public Student(String name){ this.name = name; } public String getName(){ return name; } } class StudentServer { public StudentServer(){ Student[] s = new Student[30]; s[0] = new Student("Nick"); // LINE 01: This compiles, although prints junk System.out.println(s[0]); // LINE 02: I get a error called cannot find symbol System.out.println(s[0].getName()); } public static void main(){ new StudentServer(); } } Many Thanks

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• % confuses python raw sql query

  - by Jonathan

  Following this SO question, I'm trying to "truncate" all tables related to a certain django application using the following raw sql commands in python: cursor.execute("set foreign_key_checks = 0") cursor.execute("select concat('truncate table ',table_schema,'.',table_name,';') as sql_stmt from information_schema.tables where table_schema = 'my_db' and table_type = 'base table' AND table_name LIKE 'some_prefix%'") for sql in [sql[0] for sql in cursor.fetchall()]: cursor.execute(sql) cursor.execute("set foreign_key_checks = 1") Alas I receive the following error: C:\dev\my_project>my_script.py Traceback (most recent call last): File "C:\dev\my_project\my_script.py", line 295, in <module> cursor.execute(r"select concat('truncate table ',table_schema,'.',table_name,';') as sql_stmt from information_schema.tables where table_schema = 'my_db' and table_type = 'base table' AND table_name LIKE 'some_prefix%'") File "C:\Python26\lib\site-packages\django\db\backends\util.py", line 18, in execute sql = self.db.ops.last_executed_query(self.cursor, sql, params) File "C:\Python26\lib\site-packages\django\db\backends\__init__.py", line 216, in last_executed_query return smart_unicode(sql) % u_params TypeError: not enough arguments for format string Is the % in the LIKE making trouble? How can I workaround it?

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• set pcl text to red

  - by ANervousTwitch

  Given the windows PCL separator page with escape character '\' (without quotes), how would i set an arbitrary line to red, and then the next line back to black?

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• .NET 4 ... Parallel.ForEach() question

  - by CirrusFlyer

  I understand that the new TPL (Task Parallel Library) has implemented the Parallel.ForEach() such that it works with "expressed parallelism." Meaning, it does not guarantee that your delegates will run in multiple threads, but rather it checks to see if the host platform has multiple cores, and if true, only then does it distribute the work across the cores (essentially 1 thread per core). If the host system does not have multiple cores (getting harder and harder to find such a computer) then it will run your code sequenceally like a "regular" foreach loop would. Pretty cool stuff, frankly. Normally I would do something like the following to place my long running operation on a background thread from the ThreadPool: ThreadPool.QueueUserWorkItem( new WaitCallback(targetMethod), new Object2PassIn() ); In a situation whereby the host computer only has a single core does the TPL's Parallel.ForEach() automatically place the invocation on a background thread? Or, should I manaully invoke any TPL calls from a background thead so that if I am executing from a single core computer at least that logic will be off of the GUI's dispatching thread? My concern is if I leave the TPL in charge of all this I want to ensure if it determines it's a single core box that it still marshalls the code that's inside of the Parallel.ForEach() loop on to a background thread like I would have done, so as to not block my GUI. Thanks for any thoughts or advice you may have ...

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• Python sqlite3 and concurrency

  - by RexE

  I have a Python program that uses the "threading" module. Once every second, my program starts a new thread that fetches some data from the web, and stores this data to my hard drive. I would like to use sqlite3 to store these results, but I can't get it to work. The issue seems to be about the following line: conn = sqlite3.connect("mydatabase.db") If I put this line of code inside each thread, I get an OperationalError telling me that the database file is locked. I guess this means that another thread has mydatabase.db open through a sqlite3 connection and has locked it. If I put this line of code in the main program and pass the connection object (conn) to each thread, I get a ProgrammingError, saying that SQLite objects created in a thread can only be used in that same thread. Previously I was storing all my results in CSV files, and did not have any of these file-locking issues. Hopefully this will be possible with sqlite. Any ideas?

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• Inserting a newline into a pre tag (IE, Javascript)

  - by Itay

  In IE when I insert text into a <pre> tag the newlines are ignored: <pre id="putItHere"></pre> <script> function putText() { document.getElementById("putItHere").innerHTML = "first line\nsecond line"; } </script> Using \r\n instead of a plain \n does not work. <br/> does work but inserts an extra blank line in FF, which is not acceptable for my purposes.

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• understanding and implementing Boids

  - by alphablender

  So I'm working on porting Boids to Brightscript, based on the pseudocode here: http://www.kfish.org/boids/pseudocode.html I'm trying to understand the data structures involved, for example is Velocity a single value, or is it a 3D value, ie velocity={x,y,z} It seems as if the pseudocode seems to mix this up where sometimes it has an equation that incudes both vectors and single-value items: v1 = rule1(b) v2 = rule2(b) v3 = rule3(b) b.velocity = b.velocity + v1 + v2 + v3 If Velocity is a tripartite value then this would make sense, but I'm not sure. So my first question here is, is this the correct datastructure for a single boid based on the Pseudocode on that page: boid={position:{px:0,py:0,pz:0},velocity:{x:0,y:0,z:0},vector:{x:0,y:0,z:0},pc:{x:0,y:0,z:0},pv:{x:0,y:0,z:0}) where pc=perceived center, pv= perceived velocity I"ve implemented a vector_add, vector_sub, vector_div, and vector boolean functions. The reason I'm starting from this pseudocode is I've not been able to find anything else that is as readable, but it still leaves me with lots of questions as the data structures are not explicitly defined for each variable. (edit) here's a good example of what i'm talking about: IF |b.position - bJ.position| < 100 THEN if b.position - b[j].position are both 3D coordinates, how can they be considered "less than 100" unless they are < {100,100,100} ? Maybe that is what I need to do here, use a vector comparison function?

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• Why does this simple bash code give a syntax error?

  - by Tim

  I have the following bash code, which is copied and pasted from "bash cookbook" (1st edition): #!/bin/bash VERBOSE=0; if [[ $1 =-v ]] then VERBOSE=1; shift; fi When I run this (bash 4.0.33), I get the following syntax error: ./test.sh: line 4: conditional binary operator expected ./test.sh: line 4: syntax error near `=-v' ./test.sh: line 4: `if [[ $1 =-v ]]' Is this as simple as a misprint in the bash cookbook, or is there a version incompatibility or something else here? What would the most obvious fix be? I've tried various combinations of changing the operator, but I'm not really familiar with bash scripting.

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• Output of free -m on a Linux server

  - by cat pants

  I can see from this page here: http://www.linuxatemyram.com/ That the correct amount of free ram is on the "-/+ buffers/cache" line. The extra ram being used is for disk caching. However, I noticed that the total amount of memory used listed in "-/+ buffers/cache" line is significantly less than the sum total of the "RES" column of the processes shown in top. And AFAIK, the "RES" column is how much physical memory is being used by a process. How do you explain this discrepancy?

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• Svn: how to remove all deleted files from repository ?

  - by Patrick

  I have a script in which I add all new files before to commit my working copy to my repository with this line: svn status | grep ^\? | awk '{print $2}' | xargs svn add I now want to add a line that delete from repository all deleted files in my working copy. In other terms, I cannot specify them one by one, and I need to detect them with svn status and then automatically remove them. However the line doesn't work. svn status | grep ^\! | awk '{print $2}' | xargs svn --force delete As you can see I've replaced "?" with "!" and "add" with "--force delete" Could you tell me why it doesn't work ? ps. I know it is a risky procedure. I've already discussed all about it. thanks thanks

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• OSError: [Error 1] Operation not permitted

  - by user1357576

  I am trying to run a python script which uses a binary file (xFiles.bin.addr_patched) created by a postlinker. However, I am getting this error. File "abc.py", line 74, in ParseCmd shutil.copy(gOptions.inputX, gWorkingXFile) File "/usr/lib/python2.6/shutil.py", line 89, in copy copymode(src, dst) File "/usr/lib/python2.6/shutil.py", line 66, in copymode os.chmod(dst, mode) OSError: [Errno 1] Operation not permitted: 'myPath/xFiles.bin.addr_patched' When I checked the permissions of this xFiles.bin, by ls-l, it shows that -rwxrwxrwx 1 nobody nogroup I presume the error is because this file was created by some other application, the python script I am running does not have access to it. Since I am beginner wrt ubuntu, I don't really know how to fix it. Any suggestions on how to fix this? SOLVED: As one of the answers Suggested : chown username:groupname file name fixes this issue

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• Strange macro declaration in C

  - by Andrey Atapin

  Exploring libusb-1.0.9 source code, I have found such line (./os/poll_windows.c:78): #define CHECK_INIT_POLLING do {if(!is_polling_set) init_polling();} while(0) As for me this is the same like: #define CHECK_INIT_POLLING if(!is_polling_set) init_polling(); Is there any reason to loop that expression? UPDATE: I couldn't still realize what'd be wrong after the answers, and the following example helped: #include <stdio.h> #define TEST if(test) foo(); #define TEST_DO do { if(test) foo(); } while(0) int test = 1; void foo() { printf("%s", "Foo called"); } int main(int argc, char** argv) { if(argc > 1) TEST_DO; /* LINE 12 */ else printf("%s", "skipping..."); return 0; } If you put TEST at line 12, a compiler will give an error "error: ‘else’ without a previous ‘if’". Hope, this will help someone.

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• Java - Reg. Ex. File Question

  - by aloh

  I'm grabbing lines from a text file and sifting line by line using regular expressions. I'm trying to search for blank lines, meaning nothing or just whitespace. However, what exactly is empty space? I know that whitespace is \s but what is a line that is nothing at all? null (\0)? newline (\n)? I tried the test harness in the Java tutorial to try and test to see what an empty space is but no luck so far.

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• Why can't we use strong ref cursor with dynamic SQL Statement?

  - by Vineet

  Hi ALL, I am trying to use a strong ref cur with dynamic sql statment but it is giving out an error,but when i use weak cursor it works,Please explain what is the reason and please forward me any link of oracle server architect containing matter about how compilation and parsing is done in Oracle server. THIS is the error along with code. ERROR at line 6: ORA-06550: line 6, column 7: PLS-00455: cursor 'EMP_REF_CUR' cannot be used in dynamic SQL OPEN statement ORA-06550: line 6, column 2: PL/SQL: Statement ignored declare type ref_cur_type IS REF CURSOR RETURN employees%ROWTYPE; --Creating a strong REF cursor,employees is a table emp_ref_cur ref_cur_type; emp_rec employees%ROWTYPE; BEGIN OPEN emp_ref_cur FOR 'SELECT * FROM employees'; LOOP FETCH emp_ref_cur INTO emp_rec; EXIT WHEN emp_ref_cur%NOTFOUND; END lOOP; END;

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