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  • Can anyone tell me why these lines are not working?

    - 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 "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in 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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  • The truth value of an array with more than one element is ambigous when trying to index an array

    - by user1440194
    I am trying to put all elements of rbs into a new array if the elements in var(another numpy array) is =0 and <=.1 . However when I try the following code I get this error: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() rbs = [ish[4] for ish in realbooks] for book in realbooks: var -= float(str(book[0]).replace(":", "")) bidsred = rbs[(var <= .1) and (var >=0)] any ideas on what I'm doing wrong?

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  • file output in python giving me garbage

    - by Richard
    When I write the following code I get garbage for an output. It is just a simple program to find prime numbers. It works when the first for loops range only goes up to 1000 but once the range becomes large the program fail's to output meaningful data output = open("output.dat", 'w') for i in range(2, 10000): prime = 1 for j in range(2, i-1): if i%j == 0: prime = 0 j = i-1 if prime == 1: output.write(str(i) + " " ) output.close() print "writing finished"

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  • Find the closest palindrome number C#

    - by user294837
    Hi All, I am trying to create a console application that reads number from a file all underneath each other like so: 101 9 and then outputs into another file the closest palindrome number. So far what I have is not quite rightm i.e. I don't think I can put the class inside a method which is a bit more Java I was wandering if anyone could help at all? Thanks :) namespace PalidromeC { class Program { static public void Main(string[] args) { #region WriteAnswers try { StreamWriter sw = new StreamWriter("C://Temp/PalindromeAnswers.txt"); sw.WriteLine("Answers"); sw.Close(); }//try catch (Exception e) { Console.WriteLine("Exception: " + e.Message); }//catch #endregion #region ReadFile try { string numbers; StreamReader sr = new StreamReader("C://Temp/Palindrome.txt"); numbers = sr.ReadLine(); while (numbers != null) { Console.WriteLine(numbers); numbers = sr.ReadLine(); }//while sr.Close(); Console.ReadLine(); }//try catch (Exception e) { Console.WriteLine("Exception: " + e.Message); }//catch #endregion NearPalindromeFinder f = new NearPalindromeFinder(); int palindrome = f.findNearPalindrome(n); Console.WriteLine("Nearest Palindrome = " + palindrome); }//main public static void testFindNearestPalindrome(int n) { class NearPalindromeFinder { int findNearPalindrome(int start) { if (testPalindrome(start)) return start; else { int neg = start; int pos = start; for (int i = 0; i < start; i++) { if (testPalindrome(start-i)) { neg = start-i; break; }//if if (testPalindrome(start+i)) { pos = start+i; break; }//if }//for return (start == neg) ? pos : neg; }//else }//findNearPalindrome bool testPalindrome(int start) { if (start == 0 || start == 1) return true; String str = String.valueOf(start); String rev = new if (str.equals(rev)) return true; else return false; }//testPalindrome }//NearPalindromeFinder class }//testFindNearestPalindrome }//Program Class

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  • c++, object life-time of anonymous (unnamed) variables

    - by Joe Steeve
    In the following code, the object constructed in the last line of 'main()', seems to be destroyed before the end of the expression. The destructor is called before the '<<' is executed. Is this how it is supposed to be? #include <string> #include <sstream> #include <iostream> using std::string; using std::ostringstream; using std::cout; class A : public ostringstream { public: A () {} virtual ~A () { string s; s = str(); cout << "from A: " << s << std::endl; } }; int main () { string s = "Hello"; A os; os << s; cout << os.str() << std::endl; A() << "checking this"; } This is the output: Hello from A: 0x80495f7 from A: Hello This is the gdb log: (gdb) b os.cxx : 18 Breakpoint 1 at 0x80492b1: file os.cxx, line 18. (2 locations) (gdb) r Starting program: /home/joe/sandbox/test/os Hello Breakpoint 1, ~A (this=0xbffff37c, __in_chrg=<value optimized out>, __vtt_parm=<value optimized out>) at os.cxx:18 18 cout << "from A: " << s << std::endl; (gdb) p s.c_str () $1 = 0x804b45c "0x80495f7" (gdb) p *s.c_str () $2 = 48 '0' (gdb) c Continuing. from A: 0x80495f7 Breakpoint 1, ~A (this=0xbffff2bc, __in_chrg=<value optimized out>, __vtt_parm=<value optimized out>) at os.cxx:18 18 cout << "from A: " << s << std::endl; (gdb) p s.c_str () $3 = 0x804b244 "Hello" (gdb) p *s.c_str () $4 = 72 'H' (gdb) c Continuing. from A: Hello Program exited normally. (gdb)

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  • VB.NET: question about "using" block

    - by Craig Johnston
    Consider the code: On Error Goto ErrorHandler Using sr As StreamReader = New StreamReader(OpenFile) str = sr.ReadToEnd sr.Close() End Using Exit Sub ErrorHandler: If there is an error inside the Using block how do you clean up the sr object? The sr object is not in scope in ErrHandler so sr.Close() cannot be called. Does the Using block cleanup any resources automatically even if there is an error?

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  • Connecting slots and events in PyQt4 in a loop

    - by LukaD
    Im trying to build a calculator with PyQt4 and connecting the 'clicked()' signals from the buttons doesn't as expected. Im creating my buttons for the numbers inside a for loop where i try to connect them afterwards. def __init__(self): for i in range(0,10): self._numberButtons += [QPushButton(str(i), self)] self.connect(self._numberButtons[i], SIGNAL('clicked()'), lambda : self._number(i)) def _number(self, x): print(x) When I click on the buttons all of them print out '9'. Why is that so and how can i fix this?

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  • finding and returning a string with a specified prefix

    - by tipu
    I am close but I am not sure what to do with the restuling match object. If I do p = re.search('[/@.* /]', str) I'll get any words that start with @ and end up with a space. This is what I want. However this returns a Match object that I dont' know what to do with. What's the most computationally efficient way of finding and returning a string which is prefixed with a @? For example, "Hi there @guy" After doing the proper calculations, I would be returned guy

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  • Django | how to append form field to the urlconf

    - by MMRUser
    I want to pass a form's field value to the next page (template) after user submit the page, the field could be user name, consider the following setup def form_submit(request): if request.method == 'POST': form = UsersForm(request.POST) if form.is_valid(): cd = form.cleaned_data try: newUser = form.save() return HttpResponseRedirect('/mysite/nextpage/') except Exception, ex: return HttpResponse("Ane apoi %s" % str(ex)) else: return HttpResponse('Error') "nextpage" is the template that renders after user submit the form, so I want to know how to append the form's field (user name) to the url and get that value from the view in order to pass it to the next page.. thanks.

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  • Selecting and Copying a Random File Several Times

    - by user1252778
    [Edit: see below for final code] I have the following code and I'm trying to figure out where to insert the random.choice code to make it select a single file, copy it, and repeat (here 6 times). import os import shutil import random dir_input = str(input("Enter Source Directory: ")) src_files = (os.listdir(dir_input)) for x in range (0,5): print ('This is the %d time' % x) for file_name in src_files: full_file_name = (os.path.join(dir_input, file_name)) if (os.path.isfile(full_file_name)): print ('copying...' + full_file_name) shutil.copy(full_file_name, r'C:\Dir')) else: print ('Finished!')

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  • Problem with regular expression for some special parttern.

    - by SpawnCxy
    Hi all, I got a problem when I tried to find some characters with following code: preg_match_all('/[\w\uFF10-\uFF19\uFF21-\uFF3A\uFF41-\uFF5A]/',$str,$match); //line 5 print_r($match); And I got error as below: Warning: preg_match_all() [function.preg-match-all]: Compilation failed: PCRE does not support \L, \l, \N, \U, or \u at offset 4 in E:\mycake\app\webroot\re.php on line 5 I'm not so familiar with reg expression and have no idea about this error.How can I fix this?Thanks.

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  • how to declare a public string with a textbox's text

    - by Ian Lundberg
    i am trying to do public string str = txtText.Text; but it wont let me use txtText.txt so how would I declare that so it can be used everywhere? I can't use it in the button1_click event because if I do it messes it up because I am having a string retrieve from the textbox and set to the textbox so it doesn't work right so I have to have it retrieve the textbox's text somewhere else then set to it.

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  • Splitting a list in python

    - by blob8108
    Hi, I'm writing a parser in Python. I've converted an input string into a list of tokens, such as: ['(', '2', '.', 'x', '.', '(', '3', '-', '1', ')', '+', '4', ')', '/', '3', '.', 'x', '^', '2'] I want to be able to split the list into multiple lists, like the str.split('+') function. But there doesn't seem to be a way to do my_list.split('+'). Any ideas? Thanks!

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  • JSP functions - How to declare long as parameter in TLD

    - by Spines
    I'm getting an error WARNING: Method "pl" for function "pl" not found, I think its because I'm not declaring the parameters right. <function-signature>java.lang.String pl(java.lang.Long, java.lang.String)</function-signature> is what I have in the TLD. and public static String pl(long num, String str) is what I have in the .java file.

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  • How to break the following line of python

    - by FrederikNS
    Hello Stack Overflow, I have come upon a couple of lines of code similar to this one, but I'm unsure how I should break it: blueprint = Blueprint(self.blueprint_map[str(self.ui.blueprint_combo.currentText())], runs=self.ui.runs_spin.text(), me=self.ui.me_spin.text(), pe=self.ui.pe_skill_combo.currentIndex()) Thanks in advance

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  • How to use type: "POST" in jsonp ajax call

    - by MKS
    Hi Guy, I am using JQuery ajax jsonp. I have got below JQuery Code: $.ajax({ type:"GET", url: "Login.aspx", // Send the login info to this page data: str, dataType: "jsonp", timeout: 200000, jsonp:"skywardDetails", success: function(result) { // Show 'Submit' Button $('#loginButton').show(); // Hide Gif Spinning Rotator $('#ajaxloading').hide(); } }); The above code is working fine, I just want to send the request as "POST" instead of "GET", Please suggest how can I achieve this. Thanks

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  • gae error:AttributeError: 'NoneType' object has no attribute 'user_is_member'

    - by zjm1126
    class Thread(db.Model): members = db.StringListProperty() def user_is_member(self, user): return str(user) in self.members and thread = Thread.get(db.Key.from_path('Thread', int(id))) is_member = thread.user_is_member(user) but the error is : Traceback (most recent call last): File "D:\Program Files\Google\google_appengine\google\appengine\ext\webapp\__init__.py", line 511, in __call__ handler.get(*groups) File "D:\Program Files\Google\google_appengine\google\appengine\ext\webapp\util.py", line 62, in check_login handler_method(self, *args) File "D:\zjm_code\forum_blog_gae\main.py", line 222, in get is_member = thread.user_is_member(user) AttributeError: 'NoneType' object has no attribute 'user_is_member' why ? thanks

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  • Why toInteger :: Int -> Integer is lazy?

    - by joppux
    I have the following code: {-# NOINLINE i2i #-} i2i :: Int -> Integer i2i x = toInteger x main = print $ i2i 2 Running GHC with -ddump-simpl flag gives: [Arity 1 NoCafRefs Str: DmdType U(L)] Main.i2i = GHC.Real.toInteger1 Seems that conversion from Int to Integer is lazy. Why is it so - is there a case when I can have (toInteger _|_ ::Int) /= _|_ ?

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  • JComobox is not showing in the JDialog

    - by Pujan Srivastava
    I have 2 classes. when I put bold 3 lines in the method addCourses() the dialog does not show combobox in the Panel but when I remove from addCourses and put those bold lines in the constructor, JComboBox are shown in the Panel. But data will not show because data items updates to ComboBox will happen after Constructor is created. How can I solve this problem. this.mainPanel.add(courseCombo, BorderLayout.NORTH); this.mainPanel.add(sessionCombo, BorderLayout.CENTER); this.mainPanel.add(courseButton, BorderLayout.SOUTH); public class Updator { CourseListFrame clf = new CourseListFrame(); for(...){ clf.addContentsToBox(displayName, className); } clf.addCourses(); } and second class is public class CourseListFrame extends JDialog implements ActionListener { public JPanel mainPanel = new JPanel(new BorderLayout(2, 2)); public JButton courseButton = new JButton(("Submit")); public JComboBox courseCombo; public JComboBox sessionCombo; public Multimap<String, String> map; // = HashMultimap.create(); public static CourseListFrame courseListDialog; public CourseListFrame() { super(this.getMainFrame()); this.getContentPane().add(mainPanel); map = HashMultimap.create(); courseCombo = new JComboBox(); courseCombo.addItem("Select Courses"); courseCombo.addActionListener(this); sessionCombo = new JComboBox(); } public void addContentsToBox(String course, String session) { map.put(course, session); courseCombo.addItem(course); } public void actionPerformed(ActionEvent e) { JComboBox cb = (JComboBox) e.getSource(); String str = (String) cb.getSelectedItem(); setSessionCombo(str); } public void setSessionCombo(String course) { if (map.containsKey(course)) { sessionCombo.removeAllItems(); Iterator it = map.get(course).iterator(); while (it.hasNext()) { sessionCombo.addItem(it.next()); } } } public void addCourses() { this.mainPanel.add(courseCombo, BorderLayout.NORTH); this.mainPanel.add(sessionCombo, BorderLayout.CENTER); this.mainPanel.add(courseButton, BorderLayout.SOUTH); } public static void showCourseListDialog() { if (courseListDialog == null) { courseListDialog = new CourseListFrame(); } courseListDialog.pack(); courseListDialog.setVisible(true); courseListDialog.setSize(260, 180); } }

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  • Python: inserting double or single quotes around a string

    - by Jessy
    Im using python to access a MySQL database and im getting a unknown column in field due to quotes not being around the variable. code below: cur = x.cnx.cursor() cur.execute('insert into tempPDBcode (PDBcode) values (%s);' % (s)) rows = cur.fetchall() How do i manually insert double or single quotes around the value of s? I've trying using str() and manually concatenating quotes around s but it still doesn't work. The sql statement works fine iv double and triple check my sql query.

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  • Providing updating suggestions list with javascript, php and ajax

    - by user1104854
    I'm trying to modify this example on making a live updating list to integrate it with my API. So, instead of using GET on the page with the form, I'd like to send it to that page via a function call. So, here's my form // message.php //function to display the hint sent from gethint.php function message_hint($hint){ echo $hint; } //displays the form for sending messages function send_message_form($to_user,$title,$message){ include 'gethint.php'; ?> <table> <form name = "send_message" method="post"> <td>Send A Message</td> <tr><td>To:</td><td><input type = "text" size="50" name="to_user" id = "to_user" value ="<? echo $to_user; ?>" onkeyup="showHint(this.value)"></td></tr> <tr><td>Title:</td><td><input type = "text" size="50" name="message_title"></td></tr> <tr><td>Message:</td><td><textarea rows="4" cols="50" name="message_details"></textarea></td></tr> <tr><td><input type="submit" name="submit_message"></td></tr> </table> </form> <? } Here's the head of message.php <head> <script> function showHint(str){ var to_user = document.getElementById("to_user").value //to_user is the id of the textbox if (str.length==0){ to_user.innerHTML=""; return; } if (window.XMLHttpRequest){// code for IE7+, Firefox, Chrome, Opera, Safari xmlhttp=new XMLHttpRequest(); }else{// code for IE6, IE5 xmlhttp=new ActiveXObject("Microsoft.XMLHTTP"); } xmlhttp.onreadystatechange=function(){ if (xmlhttp.readyState==4 && xmlhttp.status==200){ alert(to_user) //properly displays the name via alert box to_user.innerHTML=xmlhttp.responseText; } } xmlhttp.open("GET","gethint.php?q="+to_user,true); xmlhttp.send(); } </script> </head> The page gethint.php is exactly the same, aside from this at the bottom. //echo $response //this was the original output $message = new messages; $message->message_hint($response);

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  • applying apply() to deeply embeded list elements only

    - by romunov
    I would like to apply my function to only elements that are deeper in the list structure. For example, I would like to apply a certain function to list elements of second order only. Is this feasible with apply()? > str(l) List of 3 $ :List of 2 ..$ : num 5 ..$ : num 10 $ :List of 2 ..$ : num 15 ..$ : num 20 $ :List of 2 ..$ : num 25 ..$ : num 30

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