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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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  • java tracing spaghetti code

    - by Amarsh
    Folks, I have just joined this company which has a huge source tree based upon JSP/Servlet and EJB 1.2. No documentation exists. The code has been written over seven years, with a large number of undocumented changes. Are there any tool tah can assist me in tracing the execution? Putting a breakpoint is not helping me much.

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  • ASP.NET Repeater and DataBinder.Eval

    - by Fernando
    I've got a <asp:Repeater> in my webpage, which is bound to a programatically created dataset. The purpose of this repeater is to create an index from A-Z, which, when clicked, refreshes the information on the page. The repeater has a link button like so: <asp:LinkButton ID="indexLetter" Text='<%#DataBinder.Eval(Container.DataItem,"letter")%>' runat="server" CssClass='<%#DataBinder.Eval(Container.DataItem, "cssclass")%>' Enabled='<%#DataBinder.Eval(Container.DataItem,"enabled")%>'></asp:LinkButton> The dataset is created the following way: protected DataSet getIndex(String index) { DataSet ds = new DataSet(); ds.Tables.Add("index"); ds.Tables["index"].Columns.Add("letter"); ds.Tables["index"].Columns.Add("cssclass"); ds.Tables["index"].Columns.Add("enabled"); char alphaStart = Char.Parse("A"); char alphaEnd = Char.Parse("Z"); for (char i = alphaStart; i <= alphaEnd; i++) { String cssclass="", enabled="true"; if (index == i.ToString()) { cssclass = "selected"; enabled = "false"; } ds.Tables["index"].Rows.Add(new Object[3] {i.ToString(),cssclass,enabled }); } return ds; } However, when I run the page, a "Specified cast is not valid exception" is thrown in Text='<%#DataBinder.Eval(Container.DataItem,"letter")'. I have no idea why, I have tried manually casting to String with (String), I've tried a ToString() method, I've tried everything. Also, if in the debugger I add a watch for DataBinder.Eval(Container.DataItem,"letter"), the value it returns is "A", which according to me, should be fine for the Text Property. EDIT: Here is the exception: System.InvalidCastException was unhandled by user code Message="Specified cast is not valid." Source="App_Web_cmu9mtyc" StackTrace: at ASP.savecondition_aspx._DataBinding_control7(Object sender, EventArgs e) in e:\Documents and Settings\Fernando\My Documents\Visual Studio 2008\Projects\mediTrack\mediTrack\saveCondition.aspx:line 45 at System.Web.UI.Control.OnDataBinding(EventArgs e) at System.Web.UI.Control.DataBind(Boolean raiseOnDataBinding) at System.Web.UI.Control.DataBind() at System.Web.UI.Control.DataBindChildren() InnerException: Any advice will be greatly appreciated, thank you EDIT 2: Fixed! The problem was not in the Text or CSS tags, but in the Enabled tag, I had to cast it to a Boolean value. The problem was that the exception was signaled at the Text tag, I don't know why

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  • Makefiles, symlinked folder & relative paths

    - by l.thee.a
    Let say I have the following folders: /A/C /D/B/E /D/B/C (this is a symlink to /A/C created by ln -s) When one of the makefiles tries to use the path /D/B/C/../E it gets a "no file or directory" error. I understand why this happens; /A/E does not exist. However I have to use symlinks to populate the B folder and create the build tree (very long story). Any ideas?

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  • Linux distro name parsing

    - by Ockonal
    Hello, I chose this way to get linux distro name: ls /etc/*release And now I have to parse it for name: /etc/<name>-release def checkDistro(): p = Popen('ls /etc/*release' , shell = True, stdout = PIPE) distroRelease = p.stdout.read() distroName = re.search( ur"\/etc\/(.*)\-release", distroRelease).group() print distroName But this prints the same string that is in distroRelease.

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  • Functional programming approach for Java's input/output streams

    - by Elazar Leibovich
    I'm using Java's DataInputStream with scala to parse some simple binary file (which is very bad exprerience due to the lack of unsigned types, even in scala, but that's a different story). However I find myself forced to use mutable data structure, since Java's streams are inherently state preserving entities. What's a good design to wrap Java's streams with nice functional data structure?

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  • NSXMLParser on the iPhone, how do i use it given a xml file (newb here :\)

    - by Kenneth
    Hey guys, was wondering how do i use the NSXML parser. so lets say given i have a simple xml file with elements like 1/1/1000 14:15:16 How could i use the NSXMLParser to parse the XML File(Its on locally btw, desktop), check through each element and store each of them in an array either to be displayed/used later? I was looking through some documentation about it and i absolutely have no idea on how to use the parser i know that there are 3 methods(or more ,please correct me if im wrong) that can be overridden -..etc didStartElement -..etc didEndElement -..etc foundCharacters

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  • cmake and parallel building with "make -jN"

    - by Roman D
    Hi all, I'm trying to setup a parallel CMake-based build for my source tree, but when I issue $ cmake . $ make -j2 I get a jobserver unavailable: using -j1. Add '+' to parent make rule warning. Does anyone have an idea if it is possible to fix it somehow?

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  • solr range query errors

    - by mquinsland
    http://localhost:8983/solr/select?wt=json&q=lat:[35%20to%2038] results in **org.apache.lucene.queryParser.ParseException: Cannot parse 'lat:[35 to 38]': Encountered " "38 "" at line 1, column 11. Was expecting: "]" This is a pretty basic range query and this error will prevent us from using SOLR for our projects

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  • Skip Lists -- ever used them?

    - by Head Geek
    I'm wondering whether anyone here has ever used a skip list. It looks to have roughly the same advantages as a balanced binary tree, but is simpler to implement. If you have, did you write your own, or use a pre-written library (and if so, what was its name)?

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  • C# equivalent of NaN or IsNumeric

    - by johnc
    This seems like a fairly simple question, and I'm surprised not to have required it before. What is the most efficient way of testing a string input is a numeric (or conversely Not A Number). I guess I can do a Double.Parse or a regex (see below) public static bool IsNumeric(this string value) { return Regex.IsMatch(value, "^\\d+$"); } but I was wondering if there was a implemented way to do it, such as javascript's NaN() or IsNumeric() (was that VB, I can't remember).

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  • In Ruby, how does one get their IP octet without going through DNS?

    - by user30997
    I can, on some of my systems, get my IP address (192.68.m.n format) by doing this: addr = IPSocket::getAddress(Socket.gethostname()) ...the trouble is that this only works if the name the local machine uses for itself is the name the DNS server associates with it. How *&#( hard can it be for ruby to just return its primary interface's IP address? I have to do this in a platform-independant way or I'd just call ifconfig or ipconfig and parse it.

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  • String Parsing in C#

    - by Betamoo
    What is the most efficient way to parse a C# string in the form of "(params (abc 1.3)(sdc 2.0)....)" into a struct in the form struct Params { double abc,sdc....; } Thanks EDIT The structure always have the same parameters (number and names).. but the order is not granted..

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  • PHP object class variable

    - by mck89
    I have built a class in PHP and I must declare a class variable as an object. Everytime I want to declare an empty object I use: $var=new stdClass; But if I use it to declare a class variable as class foo { var $bar=new stdClass; } a parse error occurs. Is there a way to do this or must I declare the class variable as an object in the constructor function? PS: I'm using PHP 4.

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  • Query a stored procedure for it's parameter names and types

    - by ho1
    Is there any easy way to query a stored procedure (Oracle - PL/SQL) for what parameters it expects? I know that I can query USER_SOURCE to get the whole procedure but I'd then have to parse the whole procedure, and if the parameter is of type [table].[column]%TYPE I'd then have to query the table schema as well. Either using just sql or via ODP.Net.

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  • How do I use multiple where clauses in GHCi?

    - by T.R.
    I'm playing around with GHCi for the first time, and I'm having some trouble writing multi-line functions. My code is as follows: Prelude> :{ Prelude| let diffSquares lst = abs $ squareOfSums lst - sumOfSquares lst Prelude| where Prelude| squareOfSums lst = (fst (sumsAndSquares lst))^2 Prelude| sumOfSquares lst = snd (sumsAndSquares lst) Prelude| sumsAndSquares = foldl (\(sms,sqrs) x -> (sms+x,sqrs+x^2)) (0,0) Prelude| :} It gives the following error: <interactive>:1:142: parse error on input `=' Could someone kindly point me in the direction of what I'm missing?

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  • Question on using Informa RSS Library

    - by molleman
    hello guys I Just started looking at this technology , but i am finding it hard to understand, i want to just reed in a simple rss feed url, and display its contents how could i do this? this is what i lloked at so far URL inpFile = new URL("feed://images.apple.com/main/rss/hotnews/hotnews.rss"); ChannelIF channel = FeedParser.parse(new ChannelBuilder(), inpFile); System.out.println(channel.getDescription()); this creates a malformed url exeception, can anyone help me???

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