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• 50 sequences in one line

  - by user343934

  I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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• Querying Two Tables At Once

  - by John

  Hello, I am trying to do what I believe is called a join query. First, in a MySQL table called "login," I want to look up what "loginid" is in the record where "username" equals $profile. (This will be just one record / row in the MySQL table). Then, I want to take that "loginid" and look up all rows / records in a different MySQL table called "submission," and pull data that have that "loginid." This could possibly be more than one record / row. How do I do this? The code below doesn't seem to work. Thanks in advance, John $profile = mysql_real_escape_string($_GET['profile']); $sqlStr = "SELECT l.username, l.loginid, s.loginid, s.submissionid, s.title, s.url, s.datesubmitted, s.displayurl FROM submission AS s, login AS l WHERE l.username = '$profile', s.loginid = l.loginid ORDER BY s.datesubmitted DESC";

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• .net Diagnostics best practices?

  - by mamu

  We initially didn't use any logging or debug tracing but after spending few weeks to trace down some data corruption we decided to put required Debug.Write and Trace for production and Debug.Assert So now question is What is the best practice to use debug and trace logging. I am just looking for some thing generic. public void AddRectodatabase(object record) { Debug.WriteLine(record.ToString()); Trace.WriteLine(record.ToString()); // Add it to databse Debug.Assert(true, "Use this on case by case basis"); } Is this good enough for general purpose, am i doing anything wrong in there? We want to stick with .net System.Diagnostics over other alternatives like log4net. Is there any thing else useful in System.Diagnostics?

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• Best practice for partial updates in a RESTful service

  - by magiconair

  I am writing a RESTful service for a customer management system and I am trying to find the best practice for updating records partially. For example, I want the caller to be able to read the full record with a GET request. But for updating it only certain operations on the record are allowed, like change the status from ENABLED to DISABLED. (I have more complex scenarios than this) I don't want the caller to submit the entire record with just the updated field for security reasons (it also feels like overkill). Is there a recommended way of constructing the URIs? Do I use GET, POST, PUT or is there no agreed way of doing these kind of things? When reading the REST books RPC style calls seem to be frowned upon. Thanks Frank

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• Walking a hierarchy table with Linq

  - by Retrocoder

  I have a table with two columns, GroupId and ParentId (both are GUIDS). The table forms a hierarchy so I can look for a value in the “GroupId” filed, when I have found it I can look at its ParentId. This ParentId will also appear in the GroupId of a different record. I can use this to walk up the hierarchy tree from any point to the root (root is an empty GUID). What I’d like to do is get a list of records when I know a GroupId. This would be the record with the GroupId and all the parents back to the root record. Is this possible with Linq and if so, can anyone provide a code snippet?

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• Upsert - Efficient Update or Insert in VB.Net, SQL Server

  - by HK1

  I'm trying to understand how to streamline the process of inserting a record if none exists or updating a record if it already exists. I'm not using stored procedures, although maybe that would be the most efficient way of doing this. The actual scenario in which this is necessary is saving a user preference/setting to my SettingsUser table. In MS Access I would typically pull a DAO recordset looking for the specified setting. If the recordset comes back empty then I know I need to add a new record which I can do with the same recordset object. On the other hand, if it isn't empty, I can just update the setting's value right away. In theory, this is only two database operations. What is the recommended way of doing this in .NET?

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• Data model for timesheet to task and/or timesheet to project?

  - by John

  Let's say I want to make a simple project tracking system. A manager can create a project. Then he can create tasks for that project. Team members can record the hours they work for each task or for the project as a whole. Is the following design for the t_timesheet table a good idea? timesheet_id - primary key, autoincrement project_id - not null, foreign key constraint to t_project task_id - nullable, foreign key constraint to t_task user_id - not null, foreign key constraint to t_user hours - decimal Or should I do something like this: timesheet_id - primary key, autoincrement task_id - not null, foreign key constraint to t_task user_id - not null, foreign key constraint to t_user hours - decimal In the second option, I intend to always have a record in t_task labelled "miscellaneous items" with a foreign key to the relevant t_project record. Then I'll be able to track all hours for a project that aren't for any particular task. Are any of the ideas above good? What would be better?

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• SQL trigger for audit table question

  - by mattgcon

  I am writing a trigger to audit updates and deletes in tables. I am using SQL Server 2008 My questions are, Is there a way to find out what action is being taken on a record without going through the selection phase of the deleted and inserted tables? Another question is, if the record is being deleted, how do I record within the audit table the user that is performing the delete. (NOTE: the user connected to the database is a general connection string with a set user, I need the user who is logged into either a web app or a windows app) Please help?

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• PHP e-commerce site talking to internal database for stock / ordering?

  - by CitrusTree

  Hi. I'm working on an e-commerce site (either bespoke with PHP, or using Drupal/Ubercart), and I'd like to investigate the site interacting with an internal (filemaker) database we use to manage stock and orders. Currently we manually transfer orders from the web site to our own database, and the site does not check or record changes in stock. My plan to allow the 2 to interact is as follows: Make the internal database available externaly on a machine with a fixed IP Allow external access from the site only Connect to the internal database using ODBC (or similar) Use simple queries to check stock / record stock changes / record order details Am I missing something here as this sounds quite straight forward? Is there another solution I should be taking a look at? Thanks in advance for any help or comments.

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• Simulating an identity column within an insert trigger

  - by William Jens

  I have a table for logging that needs a log ID but I can't use an identity column because the log ID is part of a combo key. create table StuffLogs { StuffID int LogID int Note varchar(255) } There is a combo key for StuffID & LogID. I want to build an insert trigger that computes the next LogID when inserting log records. I can do it for one record at a time (see below to see how LogID is computed), but that's not really effective, and I'm hoping there's a way to do this without cursors. select @NextLogID = isnull(max(LogID),0)+1 from StuffLogs where StuffID = (select StuffID from inserted) The net result should allow me to insert any number of records into StuffLogs with the LogID column auto computed. StuffID LogID Note 123 1 foo 123 2 bar 456 1 boo 789 1 hoo Inserting another record using StuffID: 123, Note: bop will result in the following record: StuffID LogID Note 123 3 bop

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• Oracle SQL Update query takes days to update

  - by B Senthil Kumar

  I am trying to update a record in the target table based on the record coming in from source. For instance, if the incoming record is present in the target table I would update them in the target else I would simply insert. I have over one million records in my source while my target has 46 million records. The target table is partitioned based on calendar key. I implement this whole logic using Informatica. I find that the Informatica code is perfectly fine looking at the Informatica session log but its in the update it takes long time (more than 5 days to update one million records). Any suggestions as to what can be done on the scenario to improve the performance?

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• saving a records containing a member of type string to a file (Delphi, Windows)

  - by wonderer

  I have a record that looks similar to: type TNote = record Title : string; Note : string; Index : integer; end; Simple. The reason I chose to set the variables as string (as opposed to an array of chars) is that I have no idea how long those strings are going to be. They can be 1 char long, 200 or 2000. Of course when I try to save the record to a type file (file of...) the compiler complains that I have to give a size to string. Is there a way to overcome this? or a way to save those records to an untyped file and still maintain a sort of searchable way? Please do not point me to possible solutions, if you know the solution please post code. Thank you

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• MVVM where does the code to load the data belong?

  - by cody

  As I wrap my head around the mvvm thing, the view is the view, and the viewmodel is 'a modal of a view' and the model are the entities we are dealing with (or at least that is my understanding). But I'm unclear as to what and when the model entities are populated. So for example: Lets say I have app that needs to create a new record in a DB. And that record should have default values to start with. Who is responsible for the new record, and getting the default values. Does this have anything to do with MVVM or is that part of a data access layer? Who calls the the viewmodel? Or for existing records when\where are the records retrieved? And saved if altered? Thanks

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• Commenting out protect_from_forgery

  - by Andy

  Hi, I was trying to use active record store but I kept getting an invalid authenticity token. Someone told me to remove my protect_from_forgery from application controller. I know that this would remove all auth tokens but I'm not sure if this is a good idea. Does active record store not need auth tokens? By the way, all I need is a way to dynamically calculate the number of users online and their session variables. If there is a better way than using active record store it would be nice to know.

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• C++ conditional compilation

  - by Shaown

  I have the following code snippet #ifdef DO_LOG #define log(p) record(p) #else #define log(p) #endif void record(char *data){ ..... ..... } Now if I call log("hello world") in my code and DO_LOG isn't defined, will the line be compiled, in other words will it eat up the memory for the string "hello world"? P.S. There are a lot of record calls in the program and it is memory sensitive, so is there any other way to conditionally compile so that it only depends on the #define DO_LOG? Thanks in advance.

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• Alternative to NOT EXISTS

  - by Dave Colwell

  Hi all, I have two tables linked by an ID column, lets call them Table A and table B. My goal is to find all the records in table A that have no record in table B. For instance: Table A: ID----Value 1-----value1 2-----value2 3-----value3 4-----value4 Table B ID----Value 1-----x 2-----y 4-----z 4-----l As you can see, record with ID = 3 does not exist in table B, so i want a query that will give me record 3 from table A. the way i am currently doing this is by saying AND NOT EXISTS (SELECT ID FROM TableB) but since the tables are huge, the performance on this is terrible. Also, when i tried using a Left Join where TableB.ID is null, it didnt work. Can anyone suggest an alternative?

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• How to use Zend_Cache Identifier ?

  - by ArneRie

  Hi Folks, i think iam getting crazy, iam trying to implement Zend_Cache to cache my database query. I know how it works and how to configure. But i cant find a good way to set the Identifier for the cache entrys. I have an method wich search for records in my database (based on an array with search values). /** * Find Record(s) * Returns one record, or array with objects * * @param array $search Search columns => value * @param integer $limit Limit results * @return array One record , or array with objects */ public function find(array $search, $limit = null) { $identifier = 'NoIdea'; if (!($data = $this->_cache->load($identifier))) { // fetch // save to cache with $identifier.. } But what kind of identifier can use in this situation?

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• MD5 hash validation failing for unknown reason in PHP

  - by Sennheiser

  I'm writing a login form, and it converts the given password to an MD5 hash with md5($password), then matches it to an already-hashed record in my database. I know for sure that the database record is correct in this case. However, it doesn't log me in and claims the password is incorrect. Here's my code: $password = mysql_real_escape_string($_POST["password"]); ...more code... $passwordQuery = mysql_fetch_row(mysql_query(("SELECT password FROM users WHERE email = '$userEmail'"))); ...some code... elseif(md5($password) != $passwordQuery) { $_SESSION["noPass"] = "That password is incorrect."; } ...more code after... I tried pulling just the value of md5($password) and that matched up when I visually compared it. However, I can't get the comparison to work in PHP. Perhaps it is because the MySQL record is stored as text, and the MD5 is something else?

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• Update Multiple Tables at a Time - SQL Server/T-SQL

  - by peace

  I have two tables, Customer and CustomerPhone. Single record in Customer can have multiple CustomerPhone records. As you see in the image below, Phone and Fax resides in CustomerPhone table whereas the rest of the fields resides in Customer table. If user want to edits a customer record, obviously i will have to update the record in Customer table and at least two records from CustomerPhone (Phone and Fax). I could write two update statements, one Update customerPhone and the second update Customer table. Is there a better solution?

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• how do i update database using ADODB.Recordset?

  - by every_answer_gets_a_point

  i am using excel to connect to a mysql database: Dim dpath, atime, rtime, lcalib, aname, rname, bstate, instrument As String Dim rs As ADODB.Recordset Set rs = New ADODB.Recordset ConnectDB With wsBooks rs.Open "batchinfo", oConn, adOpenKeyset, adLockOptimistic, adCmdTable Worksheets.Item("Report 1").Select dpath = Trim(Range("B2").Text) atime = Trim(Range("B3").Text) rtime = Trim(Range("B4").Text) lcalib = Trim(Range("B5").Text) aname = Trim(Range("B6").Text) rname = Trim(Range("B7").Text) bstate = Trim(Range("B8").Text) ' instrument = GetInstrFromXML(wbBook.FullName) With rs .AddNew ' create a new record ' add values to each field in the record .Fields("datapath") = dpath .Fields("analysistime") = atime .Fields("reporttime") = rtime .Fields("lastcalib") = lcalib .Fields("analystname") = aname .Fields("reportname") = rname .Fields("batchstate") = "bstate" .Fields("instrument") = "NA" .Update ' stores the new record End With what is the next step? how do i do an rs.execute?

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• How do I count the number of bytes read by TextReader.ReadLine()?

  - by Steve Guidi

  I am parsing a very large file of records (one per line, each of varying length), and I'd like to keep track of the number of bytes I've read in the file so that I may recover in the event of a failure. I wrote the following: string record = myTextReader.ReadLine(); bytesRead += record.Length; ParseRecord(record); However this doesn't work since ReadLine() strips any CR/LF characters in the line. Furthermore, a line may be terminated by either CR, LF, or CRLF characters, which means I can't just add 1 to bytesRead. Is there an easy way to get the actual line length, or do I write my own ReadLine() method in terms of the granular Read() operations?

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• How to search for duplicate values in a huge text file having around Half Million records

  - by Shibu

  I have an input txt file which has data in the form of records (each row is a record and represents more or less like a DB table) and I need to find for duplicate values. For example: Rec1: ACCOUNT_NBR_1*NAME_1*VALUE_1 Rec2: ACCOUNT_NBR_2*NAME_2*VALUE_2 Rec3: ACCOUNT_NBR_1*NAME_3*VALUE_3 In the above set, the Rec1 and Rec2 are considered to be duplicates as the ACCOUNT NUMBERS are same(ACCOUNT_NBR1). Note: The input file shown above is a delimiter type file (the delimiter being *) however the file type can also be a fixed length file where each column starts and ends with a specified positions. I am currently doing this with the following logic: Loop thru each ACCOUNT NUMBER Loop thru each line of the txt file and record and check if this is repeated. If repeated record the same in a hashtable. End End And I am using 'Pattern' & 'BufferedReader' java API's to perform the above task. But since it is taking a long time, I would like to know a better way of handling it. Thanks, Shibu

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• how to handle exceptions/errors in php?

  - by fayer

  when using 3rd part libraries they tend to throw exceptions to the browser and hence kill the script. eg. if im using doctrine and insert a duplicate record to the database it will throw an exception. i wonder, what is best practice for handling these exceptions. should i always do a try...catch? but doesn't that mean that i will have try...catch all over the script and for every single function/class i use? Or is it just for debugging? i don't quite get the picture. Cause if a record already exists in a database, i want to tell the user "Record already exists". And if i code a library or a function, should i always use "throw new Expcetion($message, $code)" when i want to create an error? Please shed a light on how one should create/handle exceptions/errors. Thanks

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• Code won't exit foreach block

  - by Matt

  I've got the following C# code segment that takes a list, finds objects that are ready to update, then shoves them into a temp list, deletes from the main list, and then goes on its merry way. My issue is that the foreach block, which cycles through my main list, won't exit. TempLog.Clear(); //Ensure TempLog is empty foreach (CLogger ready in PlayerLog) { if (ready.UpdateReady == true) // Record is ready to be updated in database { TempLog.Add(ready); // Add record to templog PlayerLog.Remove(ready); // Remove from playerlog } } <---- Never reaches this point if (TempLog.Count > 0) // Just check that templog isn't empty { new Thread(Update).Start(); // Run update code } I've put heaps of debugging in, and I can watch PlayerLog start at 1, TempLog at 0, then it enters the foreach loop, picks up that the record UpdateReady flag is on, TempLog goes to 1, PlayerLog goes to 0, then it just stops.. No errors, just stops.. Thanks for the help :)

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• Referencing surrogate key

  - by Arman

  I have a table that has an autoincrement surrogate key. I want to use it as a foreign key of my other table. The thing is, I cant figure out how I can reference it to that table, because it is nearly impossible to determine what I have to reference(the actual value of the surrogate key). Please be noted that what I am trying to do is adding a tuple/record through my program(outside the dbms). The process is: Add a new record in Table1 and generate an autoincrement key. Update Add a new record in Table2 and reference its foreign key to the primary key of Table1. Update My question is : HOW do I store the foreign key if I didnt know what is it?

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