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  • Subprocess fails to catch the standard output

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "<string>", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in <module> align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • Handling newline character in input between Windows and Linux

    - by Fazal
    I think this is a standard problem which may have been asked before but I could not get the exact answer so posting the issue. The issue is that our server is running on a linux box. We access the server over the browser on a window box to enter data into field which is supposed to contain multiple lines which user can enter by pressing the enter key after each line Abc Def GHI When this input field (this is a text area),is read on the linux machine, we want to split the data based on new line character. I had three question on this. Does the incoming data contain "\r\n" or "\n" If incoming data does contain "\r\n", the linux line.separator property (vm property) would not work for me as it would say "\n" and therefore may leave "\r" in the data. If "\r" is left in the data, if I open the file on a windows machine, will this mean a newline character? Finally can anyone tell me the standard way to deal with this issue?

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  • Problem getting puppet to sync custom fact

    - by byron-appelt
    I am having trouble getting puppet to sync a custom fact. I am using puppet version 0.25.4. The fact is inside a module as described in http://docs.reductivelabs.com/guides/plugins_in_modules.html If I specify --pluginsync on the command line it does sync correctly, but does not otherwise even though I have pluginsync=true in my puppet.conf. Is it correct that this command line option and the option in the puppet.conf should have the same behavior?

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  • When should I use indexed arrays of OpenGL vertices?

    - by Tartley
    I'm trying to get a clear idea of when I should be using indexed arrays of OpenGL vertices, drawn with gl[Multi]DrawElements and the like, versus when I should simply use contiguous arrays of vertices, drawn with gl[Multi]DrawArrays. (Update: The consensus in the replies I got is that one should always be using indexed vertices.) I have gone back and forth on this issue several times, so I'm going to outline my current understanding, in the hopes someone can either tell me I'm now finally more or less correct, or else point out where my remaining misunderstandings are. Specifically, I have three conclusions, in bold. Please correct them if they are wrong. One simple case is if my geometry consists of meshes to form curved surfaces. In this case, the vertices in the middle of the mesh will have identical attributes (position, normal, color, texture coord, etc) for every triangle which uses the vertex. This leads me to conclude that: 1. For geometry with few seams, indexed arrays are a big win. Follow rule 1 always, except: For geometry that is very 'blocky', in which every edge represents a seam, the benefit of indexed arrays is less obvious. To take a simple cube as an example, although each vertex is used in three different faces, we can't share vertices between them, because for a single vertex, the surface normals (and possible other things, like color and texture co-ord) will differ on each face. Hence we need to explicitly introduce redundant vertex positions into our array, so that the same position can be used several times with different normals, etc. This means that indexed arrays are of less use. e.g. When rendering a single face of a cube: 0 1 o---o |\ | | \ | | \| o---o 3 2 (this can be considered in isolation, because the seams between this face and all adjacent faces mean than none of these vertices can be shared between faces) if rendering using GL_TRIANGLE_FAN (or _STRIP), then each face of the cube can be rendered thus: verts = [v0, v1, v2, v3] colors = [c0, c0, c0, c0] normal = [n0, n0, n0, n0] Adding indices does not allow us to simplify this. From this I conclude that: 2. When rendering geometry which is all seams or mostly seams, when using GL_TRIANGLE_STRIP or _FAN, then I should never use indexed arrays, and should instead always use gl[Multi]DrawArrays. (Update: Replies indicate that this conclusion is wrong. Even though indices don't allow us to reduce the size of the arrays here, they should still be used because of other performance benefits, as discussed in the comments) The only exception to rule 2 is: When using GL_TRIANGLES (instead of strips or fans), then half of the vertices can still be re-used twice, with identical normals and colors, etc, because each cube face is rendered as two separate triangles. Again, for the same single cube face: 0 1 o---o |\ | | \ | | \| o---o 3 2 Without indices, using GL_TRIANGLES, the arrays would be something like: verts = [v0, v1, v2, v2, v3, v0] normals = [n0, n0, n0, n0, n0, n0] colors = [c0, c0, c0, c0, c0, c0] Since a vertex and a normal are often 3 floats each, and a color is often 3 bytes, that gives, for each cube face, about: verts = 6 * 3 floats = 18 floats normals = 6 * 3 floats = 18 floats colors = 6 * 3 bytes = 18 bytes = 36 floats and 18 bytes per cube face. (I understand the number of bytes might change if different types are used, the exact figures are just for illustration.) With indices, we can simplify this a little, giving: verts = [v0, v1, v2, v3] (4 * 3 = 12 floats) normals = [n0, n0, n0, n0] (4 * 3 = 12 floats) colors = [c0, c0, c0, c0] (4 * 3 = 12 bytes) indices = [0, 1, 2, 2, 3, 0] (6 shorts) = 24 floats + 12 bytes, and maybe 6 shorts, per cube face. See how in the latter case, vertices 0 and 2 are used twice, but only represented once in each of the verts, normals and colors arrays. This sounds like a small win for using indices, even in the extreme case of every single geometry edge being a seam. This leads me to conclude that: 3. When using GL_TRIANGLES, one should always use indexed arrays, even for geometry which is all seams. Please correct my conclusions in bold if they are wrong.

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  • Handle mysql restart in SQLAlchemy

    - by wRAR
    My Pylons app uses local MySQL server via SQLAlchemy and python-MySQLdb. When the server is restarted, open pooled connections are apparently closed, but the application doesn't know about this and apparently when it tries to use such connection it receives "MySQL server has gone away": File '/usr/lib/pymodules/python2.6/sqlalchemy/engine/default.py', line 277 in do_execute cursor.execute(statement, parameters) File '/usr/lib/pymodules/python2.6/MySQLdb/cursors.py', line 166 in execute self.errorhandler(self, exc, value) File '/usr/lib/pymodules/python2.6/MySQLdb/connections.py', line 35 in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (2006, 'MySQL server has gone away') This exception is not caught anywhere so it bubbles up to the user. If I should handle this exception somewhere in my code, please show the place for such code in a Pylons WSGI app. Or maybe there is a solution in SA itself?

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  • "Socket operation on non-socket" error due to strange syntax

    - by Robert S. Barnes
    I ran across the error Socket operation on non-socket in some of my networking code when calling connect and spent a lot of time trying to figure out what was causing it. I finally figured out that the following line of code was causing the problem: if ((sockfd = socket( ai->ai_family, ai->ai_socktype, ai->ai_protocol) < 0)) { See the problem? Here's what the line should look like: if ((sockfd = socket( ai->ai_family, ai->ai_socktype, ai->ai_protocol)) < 0) { What I don't understand is why the first, incorrect line doesn't produce a warning. To put it another way, shouldn't the general form: if ( foo = bar() < baz ) do_something(); look odd to the compiler, especially running with g++ -Wall -Wextra? If not, shouldn't it at least show up as "bad style" to cppcheck, which I'm also running as part of my compile?

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  • Script execution flow stopped?

    - by vijay.shad
    Hi all, Now my script is able to start server, But I am still have some problem with my script. When the start server command is executed, the control does not pass the line and does not execute further of that line. Please tell me what is the problem and how can I get smooth execution of the my script.

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  • Best Secure Encryption for Zip Files via Linux

    - by Daniel
    I want to use highly secure encryption for zipped files via Linux/Ubuntu using a command line terminal, what is the best command line tool to get this job done? zip -e -P PASSWORD file1 file2 file3 file4 Or 7za a file.7z *.txt -pSECRET What encryption is used and how secure is it?

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  • CSS code formatting from Autohotkey..........

    - by metal gear solid
    i need functionality of this tool in Autohotkey keyboard shortcut. If i would select all code and press AHK key combination then code should be set like this tool does. single line/ multiline. Need to AHK script for both multiline and single line http://www.newmediacampaigns.com/files/posts/css-formatting/clean.php

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  • Python Closures Example Code

    - by user336527
    I am learning Python using "Dive Into Python 3" book. I like it, but I don't understand the example used to introduce Closures in Section 6.5. I mean, I see how it works, and I think it's really cool. But I don't see any real benefit: it seems to me the same result could be achieved by simply reading in the rules file line by line in a loop, and doing search / replace for each line read. Could someone help me to: either understand why using closures in this example improves the code (e.g., easier to maintain, extend, reuse, or debug?) or suggest a source of some other real-life code examples where closures really shine? Thank you!

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  • HowTo make a marching ants border in Morphic?

    - by Helene Bilbo
    I am looking for a marching ants border or line in Morphic: Wikipedia describes a possbile algorithm: The easiest way to achieve this animation is by drawing the selection using a pen pattern that contains diagonal lines. If the selection outline is only one pixel thick, the slices out of the pattern will then look like a dashed line, and the animation can easily be achieved by simply shifting the pattern one pixel sideways and redrawing the outline. As there is probably none readymade, has anybody a hint for me how to create such a border or line? (The marching ants pattern as a GIF animation is licensed under CC by Uli Kusterer)

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  • php error: unexpected T_OBJECT_OPERATOR.... trying to install magento using ssh commands to dreamhos

    - by Jane
    I am trying to install magento (e-commerce platform) I am following a tutorial that tells me to run this command using ssh: ./pear mage-setup but i'm getting this error: Parse error: syntax error, unexpected T_OBJECT_OPERATOR in /home/domainname.com/downloader/pearlib/php/System.php on line 400 Line 400 is commented in the code snippit from the system.php file: /* Magento fix for set tmp dir in config.ini */ if (class_exists('Maged_Controller',false)) { /*line 400 */ $magedConfig = Maged_Controller::model('Config',true)->load();** if ($magedConfig->get('use_custom_permissions_mode') == '1' && $mode = $magedConfig->get('mkdir_mode')) { $result = System::mkDir(array('-m' . $mode, $tmpdir)); } else { $result = System::mkDir(array('-p', $tmpdir)); } if (!$result) { return false; } } Can anyone help my demystify this error?

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  • Monorail - Form submission using GET instead of POST

    - by Septih
    Hello, I'm writing some additions to a Castle MonoRail based site involving an Add and an Edit form. The add form works fine and uses POST but the edit form uses GET. The only major difference I can see is that the edit method is called with the Id of the object being edited in the query string. When the submit button is pressed on the edit form, the only argument passed is this object Id again. Here is the code for the edit form: <form action="edit.ashx" method="post"> <h3>Coupon Description</h3> <textarea name="comments" width="200">$comments</textarea> <br/><br/> <h3>Coupon Actions</h3> <br/> <div>Give Stories</div> <ul class="checklist" style="overflow:auto;height:144px;width:100%"> #foreach ($story in $stories.Values) <li> <label> #set ($associated = "") #foreach($storyId in $storyIds) #if($story.Id == $storyId) #set($associated = " checked='true'") #end #end <input type="checkbox" name="chk_${story.Id}" id="chk_${story.Id}" value="true" class="checkbox" $associated/> $story.Name </label> </li> #end </ul> <br/><br/> <div>Give Credit Amount</div> <input type="text" name="credit" value="$credit" /> <br/><br/> <h3>Coupon Uses</h3> <input type="checkbox" name="multi" #if($multi) checked="true" #end /> Multi-Use Coupon?<br/><br/> <b>OR</b> <br/> <br/> Number of Uses per Coupon: <input type="text" name="uses" value="$uses" /> <br/> <input type="submit" name="Save" /> </form> The differences between this and the add form is the velocity stuff to do with association and the values of the inputs being from the PropertyBag. The Method dealing with this on the controller starts like this: public void Edit(int id) { Coupon coupon = Coupon.GetRepository(User.Site.Id).FindById(id).Value; if(coupon == null) { RedirectToReferrer(); return; } IFutureQueryOfList<Story> stories = Story.GetRepository(User.Site.Id).OnlyReturnEnabled().FindAll("Name", true); if (Params["Save"] == null) { ... } } It reliably gets called but a breakpoint on the Params["Save"] lets me see that the HttpMethod is "GET" and the only arguments passed (In the Form and the Request) are the object Id and additional HTTP headers. At the end of the day I'm not that familiar with MonoRail and this may be a stupid mistake on my behalf, but I would very much appreciate being made a fool out of if it fixes the problem! :) Thanks

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  • SYSDATE - 1 error on pl/sql function

    - by ayo
    Hi curtisk/all, I have an issue: when i issue this function below ti gives me the following error: select 'EXECUTE DBMS_LOGMNR.ADD_LOGFILE(LOGFILENAME =>'''||name||'''||,OPTIONS=>DBMS_LOGMNR.NEW);' from v\$archived_log where name is not null; select 'EXECUTE DBMS_LOGMNR.ADD_LOGFILE(LOGFILENAME =>'''||name||'''||,OPTIONS=>DBMS_LOGMNR.ADDFILE);' from v\$archived_log where name is not null; EXECUTE DBMS_LOGMNR.START_LOGMNR( STARTTIME => SYSDATE - 1, ENDTIME => SYSDATE, OPTIONS => DBMS_LOGMNR.DICT_FROM_ONLINE_CATALOG + DBMS_LOGMNR.CONTINUOUS_MINE + DBMS_LOGMNR.COMMITTED_DATA_ONLY + DBMS_LOGMNR.PRINT_PRETTY_SQL); Error: * ERROR at line 1: ORA-01291: missing logfile ORA-06512: at "SYS.DBMS_LOGMNR", line 58 ORA-06512: at line 1 But i have added all the archived logs for several days before and my sysdate is at today. Kindly help out on this issue. thanks. Reagrds Ayo

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  • Use a Trendline Formula to Get Values for Any Given X with Excel

    - by kirkouimet
    Is there an easy way to apply the trend line formula from a chart to any given X value in Excel? For example, I want to get the Y value for a given X = $2,006.00. I've already taken the formula and retyped it out be: =-0.000000000008*X^3 - 0.00000001*X^2 + 0.0003*X - 0.0029 I am continually making adjustments to the trend line by adding more data, and don't want to retype out the formula every time.

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  • Visual Studio 2010 Formatting

    - by Rosarch
    I have plenty of experience with Eclipse, and now I'm trying out Visual Studio 2010. I find its formatting somewhat counter-intuitive. Here are some things I'm trying to figure out: Is there a way to select all text and format/indent it properly, like SHIFT+A SHIFT+I in Eclipse? Why is it that when I type a line like if (n == 0) {, as soon as I type the opening brace, the text cursor is moved to the beginning of the line? Is this some productivity speedup I'm failing to see? When I hit ENTER after the aforementioned line, I'd like the closing brace to be put in place automatically for me. How can I do this? I've looked for hotkey documentation, and it's helped a bit, but this still feels clunky to me.

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  • MQ EOL Data conversion

    - by lemotdit
    we are sending data trough MQ from a z/OS/CICS system to an AS400. Original encoding of the message is CCSID 500 with a MQSTR Format. The client application is getting the message with the CONVERT option and CCSID 819. Data is almost converted correctly except for the end of line caracter. Any idea? The z/OS is sending 0D (CR) as end of line caracter. If they had 0D+0A (CR+LF), CCSID automatically change from 500 to 437, and the end of line still ain't right on the client side.

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  • yiic shell: failed to perform 'crud'

    - by ufw
    Debian Squeeze, PHP 5.3.2-1, Yii 1.1.2, PHP $path to php is /usr/bin/php, permissions are '777'. When I try to run 'crud Test' in yii shell, I get the following error message: PHP Warning: include(/var/www/test/protected/models/Test.php): failed to open stream: No such file or directory in /var/www/yii/framework/YiiBase.php on line 335 PHP Warning: include(): Failed opening '/var/www/test/protected/models/Test.php' for inclusion (include_path='.:/var/www/test/protected/components:/var/www/test/protected/models:/usr/share/php:/usr/share/pear') in /var/www/yii/framework/YiiBase.php on line 335 PHP Fatal error: Class 'Test' not found in /var/www/yii/framework/db/ar/CActiveRecord.php on line 341

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  • How to draw the "trail" in a maze solving application

    - by snow-spur
    Hello i have designed a maze and i want to draw a path between the cells as the 'person' moves from one cell to the next. So each time i move the cell a line is drawn Also i am using the graphics module The graphics module is an object oriented library Im importing from graphics import* from maze import* my circle which is my cell center = Point(15, 15) c = Circle(center, 12) c.setFill('blue') c.setOutline('yellow') c.draw(win) p1 = Point(c.getCenter().getX(), c.getCenter().getY()) this is my loop if mazez.blockedCount(cloc)> 2: mazez.addDecoration(cloc, "grey") mazez[cloc].deadend = True c.move(-25, 0) p2 = Point(getX(), getY()) line = graphics.Line(p1, p2) cloc.col = cloc.col - 1 Now it says getX not defined every time i press a key is this because of p2???

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  • BULK INSERT with inconsitant number of columns

    - by aceinthehole
    I am trying to load a large amount data in SQL server from a flat file using BULK INSERT. However, my file has varying number of column, for instance the first row contains 14 and the second contains 4. That is OK, I just want to make a table with the max number of columns and load the file into it with nulls for the missing columns. I can play with it from that point. But it seems that SQL Server when reaching the end of the line and having more columns to fill for that same row in the destination table, just moves on to the next line and attempts to put the data on that line to the wrong column of the table. Is there a way to get the behavior that I am looking for? Is there a table hint that I can use the specify this? Has anyone run into this before? Here is the code BULK INSERT #t FROM '<path to file>' WITH ( DATAFILETYPE = 'char', KEEPNULLS, FIELDTERMINATOR = '#' )

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  • mod_security: another rule with same ID

    - by Ashish
    I have installed httpd 2.2.15 on CentOS 6.5 (minimal installation with no cPanel) with modsecurity 2.8. When I am starting httpd I am getting this error: Starting httpd: Syntax error on line 23 of /etc/httpd/conf.d/modsecurity.conf: ModSecurity: Found another rule with the same id The line 23 is: "id:'200000',phase:1,t:none,t:lowercase,pass,nolog,ctl:requestBodyProcessor=XML" Please advise. Thx in advanced

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  • Getting "open_basedir restriction in effect" in spite of adding the correct entry.

    - by akshat
    I am trying to create a shared hosting scenario, using open_basedir option of php. I am doing this by adding the following to apache2.conf <VirtualHost *:80> ServerName lt1.example.net DocumentRoot /home/akshat/example/tmpblogs/tb1/ php_admin_value open_basedir /home/akshat/example/tmpblogs/tb1/ </VirtualHost> <VirtualHost *:80> ServerName lt2.example.net DocumentRoot /home/akshat/example/tmpblogs/tb2/ php_admin_flag open_basedir /home/akshat/example/tmpblogs/tb2/ </VirtualHost> Now when I access lt2.example.net, I get the error: Warning: Unknown: open_basedir restriction in effect. File(/home/akshat/example/tmpblogs/tb2/index.php) is not within the allowed path(s): (0) in Unknown on line 0 Warning: Unknown: failed to open stream: Operation not permitted in Unknown on line 0 Fatal error: Unknown: Failed opening required '/home/akshat/example/tmpblogs/tb2/index.php' (include_path='.:/usr/share/php:/usr/share/pear') in Unknown on line 0 I was getting the same error while accessing "lt1.example.net" too, but then it suddenly became alright. What am I doing wrong here?

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  • ASP.net page gets error on import statement, but I do have the reference in place?

    - by Greg
    Hi, Any ideas why I am getting the below error in my MVC2 project, even through in the project itself I definitely have a reference to "system.Web.Entity"? Compiler Error Message: CS0234: The type or namespace name 'Entity' does not exist in the namespace 'System.Data' (are you missing an assembly reference?) Source Error: Line 1: <%@ Page Language="C#" Inherits="System.Web.Mvc.ViewPage<List<Node>>" %> Line 2: <%@ Import Namespace="TopologyDAL" %> Line 3: <%@ Import Namespace="System.Data.Entity" %> thanks

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  • Read tab delimited text file into MySQL table with PHP

    - by Simon S
    I am trying to read in a series of tab delimited text files into existing MySQL tables. The code I have is quite simple: $lines = file("import/file_to_import.txt"); foreach ($lines as $line_num => $line) { if($line_num > 1) { $arr = explode("\t", $line); $sql = sprintf("INSERT INTO my_table VALUES('%s', '%s', '%s', %s, %s);", trim((string)$arr[0]), trim((string)$arr[1]), trim((string)$arr[2]), trim((string)$arr[3]), trim((string)$arr[4])); mysql_query($sql, $database) or die(mysql_error()); } } But no matter what I do (hence the casting before each variable in the sprintf statement) I get the "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1" error. I echo out the code, paste it into a MySQL editor and it runs fine, it just won't execute from the PHP script. What am I doing wrong?? Si

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  • "success=n" control syntax in pam.conf / pam.d/* files ...

    - by Jamie
    After sucessfully configuring Kerberos, this is what I've found in /etc/pam.d/common-auth file: auth [success=2 default=ignore] pam_unix.so nullok_secure auth [success=1 default=ignore] pam_winbind.so krb5_auth krb5_ccache_type=FILE cached_login try_first_pass auth requisite pam_deny.so auth required pam_permit.so Does the success=2 control value mean that if the pam_unix.so fails, the authentication skips to the auth requisite pam_deny.so line or to the last line?

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