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  • Parse a text file into multiple text file

    - by Vijay Kumar Singh
    I want to get multiple file by parsing a input file Through Java. The Input file contains many fasta format of thousands of protein sequence and I want to generate raw format(i.e., without any comma semicolon and without any extra symbol like "", "[", "]" etc) of each protein sequence. A fasta sequence starts form "" symbol followed by description of protein and then sequence of protein. For example ? lcl|NC_000001.10_cdsid_XP_003403591.1 [gene=LOC100652771] [protein=hypothetical protein LOC100652771] [protein_id=XP_003403591.1] [location=join(12190..12227,12595..12721,13403..13639)] MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCL PSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH Like above formate the input file contains 1000s of protein sequence. I have to generate thousands of raw file containing only individual protein sequence without any special symbol or gaps. I have developed the code for it in Java but out put is : Cannot open a file followed by cannot find file. Please help me to solve my problem. Regards Vijay Kumar Garg Varanasi Bharat (India) The code is /*Java code to convert FASTA format to a raw format*/ import java.io.*; import java.util.*; import java.util.regex.*; import java.io.FileInputStream; // java package for using regular expression public class Arrayren { public static void main(String args[]) throws IOException { String a[]=new String[1000]; String b[][] =new String[1000][1000]; /*open the id file*/ try { File f = new File ("input.txt"); //opening the text document containing genbank ids FileInputStream fis = new FileInputStream("input.txt"); //Reading the file contents through inputstream BufferedInputStream bis = new BufferedInputStream(fis); // Writing the contents to a buffered stream DataInputStream dis = new DataInputStream(bis); //Method for reading Java Standard data types String inputline; String line; String separator = System.getProperty("line.separator"); // reads a line till next line operator is found int i=0; while ((inputline=dis.readLine()) != null) { i++; a[i]=inputline; a[i]=a[i].replaceAll(separator,""); //replaces unwanted patterns like /n with space a[i]=a[i].trim(); // trims out if any space is available a[i]=a[i]+".txt"; //takes the file name into an array try // to handle run time error /*take the sequence in to an array*/ { BufferedReader in = new BufferedReader (new FileReader(a[i])); String inline = null; int j=0; while((inline=in.readLine()) != null) { j++; b[i][j]=inline; Pattern q=Pattern.compile(">"); //Compiling the regular expression Matcher n=q.matcher(inline); //creates the matcher for the above pattern if(n.find()) { /*appending the comment line*/ b[i][j]=b[i][j].replaceAll(">gi",""); //identify the pattern and replace it with a space b[i][j]=b[i][j].replaceAll("[a-zA-Z]",""); b[i][j]=b[i][j].replaceAll("|",""); b[i][j]=b[i][j].replaceAll("\\d{1,15}",""); b[i][j]=b[i][j].replaceAll(".",""); b[i][j]=b[i][j].replaceAll("_",""); b[i][j]=b[i][j].replaceAll("\\(",""); b[i][j]=b[i][j].replaceAll("\\)",""); } /*printing the sequence in to a text file*/ b[i][j]=b[i][j].replaceAll(separator,""); b[i][j]=b[i][j].trim(); // trims out if any space is available File create = new File(inputline+"R.txt"); try { if(!create.exists()) { create.createNewFile(); // creates a new file } else { System.out.println("file already exists"); } } catch(IOException e) // to catch the exception and print the error if cannot open a file { System.err.println("cannot create a file"); } BufferedWriter outt = new BufferedWriter(new FileWriter(inputline+"R.txt", true)); outt.write(b[i][j]); // printing the contents to a text file outt.close(); // closing the text file System.out.println(b[i][j]); } } catch(Exception e) { System.out.println("cannot open a file"); } } } catch(Exception ex) // catch the exception and prints the error if cannot find file { System.out.println("cannot find file "); } } } If you provide me correct it will be much easier to understand.

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  • Designing a database file format

    - by RoliSoft
    I would like to design my own database engine for educational purposes, for the time being. Designing a binary file format is not hard nor the question, I've done it in the past, but while designing a database file format, I have come across a very important question: How to handle the deletion of an item? So far, I've thought of the following two options: Each item will have a "deleted" bit which is set to 1 upon deletion. Pro: relatively fast. Con: potentially sensitive data will remain in the file. 0x00 out the whole item upon deletion. Pro: potentially sensitive data will be removed from the file. Con: relatively slow. Recreating the whole database. Pro: no empty blocks which makes the follow-up question void. Con: it's a really good idea to overwrite the whole 4 GB database file because a user corrected a typo. I will sell this method to Twitter ASAP! Now let's say you already have a few empty blocks in your database (deleted items). The follow-up question is how to handle the insertion of a new item? Append the item to the end of the file. Pro: fastest possible. Con: file will get huge because of all the empty blocks that remain because deleted items aren't actually deleted. Search for an empty block exactly the size of the one you're inserting. Pro: may get rid of some blocks. Con: you may end up scanning the whole file at each insert only to find out it's very unlikely to come across a perfectly fitting empty block. Find the first empty block which is equal or larger than the item you're inserting. Pro: you probably won't end up scanning the whole file, as you will find an empty block somewhere mid-way; this will keep the file size relatively low. Con: there will still be lots of leftover 0x00 bytes at the end of items which were inserted into bigger empty blocks than they are. Rigth now, I think the first deletion method and the last insertion method are probably the "best" mix, but they would still have their own small issues. Alternatively, the first insertion method and scheduled full database recreation. (Probably not a good idea when working with really large databases. Also, each small update in that method will clone the whole item to the end of the file, thus accelerating file growth at a potentially insane rate.) Unless there is a way of deleting/inserting blocks from/to the middle of the file in a file-system approved way, what's the best way to do this? More importantly, how do databases currently used in production usually handle this?

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  • Best MAILING LIST solution for a CONFERENCE and its 400 participants

    - by Ole Morten Amundsen
    Dear community, what would you recommend for mailling lists? The conference is non-profit, named Smidig2010 (=Agile2010 in norwegian), will have about 400-500 participants 16.-17.november. At the time of writing this, we have not opened for registration, but would like people to be able to participate, ask questions, get informed and get inspired. We've used a forum before, but forums don't seem to be a good fit for this. I would like to set up a mailinglist, It'll have to be KISS, for the users: enter your email (a input box at our site smidig2010.no) get a confirmation mail, click a link. start posting, reading through archives, answering others etc. I like the look and feel of googlegroups, but I don't like the signup/account creation overhead imposed on the user. I've heard you may combine googlegroups with mailman and stuff, but, yeah, I can't believe our own incompetence on this subject! Btw, we are mostly developers and the conference app is being written in ruby on rails. Being non-profit, we prefer free, but we take everything into consideration. Any suggestions?

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  • R: how can I concatenate a list?

    - by John
    I'm trying to produce a single variable which is a concatenation of two chars e.g to go from "p30s4" "p28s4" to "p30s4 p28s4". I've tried cat and paste as shown below. Both return empty variables. What am I doing wrong? > blah = c("p30s4","p28s4") > blah [1] "p30s4" "p28s4" > foo = cat(blah) p30s4 p28s4 > foo NULL > foo = paste(cat(blah)) p30s4 p28s4 > foo character(0)

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  • How can I also add class to the last list for the second list block in IE?

    - by user244394
    Hi All I have 2 list and i want to add a class ="last" to the list item 5 for both. they seem to work fine on firefox. it add green to both list item 5. But in IE7 it adds only the first list item 5, not the second How can I also add class last it to the second list block as well for IE? .last{background-color: green} jQuery( document ).ready( function () { // Add first and last menu item classes $('ul.menu li:first-child').addClass( 'first_item' ); $('#menu li:last-child').addClass( 'last' ); }); list item 1 list item 2 list item 3 list item 4 list item 5 list item 1 list item 2 list item 3 list item 4 list item 5

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  • Reading data from text file in C

    - by themake
    I have a text file which contains words separated by space. I want to take each word from the file and store it. So i have opened the file but am unsure how to assign the word to a char. FILE *fp; fp = fopen("file.txt", "r"); //then i want char one = the first word in the file char two = the second word in the file

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  • C++ Constructor initialization list strangeness

    - by Andy
    I have always been a good boy when writing my classes, prefixing all member variables with m_: class Test { int m_int1; int m_int2; public: Test(int int1, int int2) : m_int1(int int1), m_int2(int int2) {} }; void main() { Test t(10, 20); // Just an example } However, recently I forgot to do that and ended up writing: class Test { int int1; int int2; public: // Very questionable, but of course I meant to assign ::int1 to this->int1! Test(int int1, int int2) : int1(int1), int2(int2) {} }; Believe it or not, the code compiled with no errors/warnings and the assignments took place correctly! It was only when doing the final check before checking in my code when I realised what I had done. My question is: why did my code compile? Is something like that allowed in the C++ standard, or is it simply a case of the compiler being clever? In case you were wondering, I was using Visual Studio 2008 Thank you.

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  • Python recursion with list returns None

    - by newman
    def foo(a): a.append(1) if len(a) > 10: print a return a else: foo(a) Why this recursive function returns None (see transcript below)? I can't quite understand what I am doing wrong. In [263]: x = [] In [264]: y = foo(x) [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] In [265]: print y None

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  • opening and viewing a file in php

    - by Christian Burgos
    how do i open/view for editing an uploaded file in php? i have tried this but it doesn't open the file. $my_file = 'file.txt'; $handle = fopen($my_file, 'r'); $data = fread($handle,filesize($my_file)); i've also tried this but it wont work. $my_file = 'file.txt'; $handle = fopen($my_file, 'w') or die('Cannot open file: '.$my_file); $data = 'This is the data'; fwrite($handle, $data); what i have in mind is like when you want to view an uploaded resume,documents or any other ms office files like .docx,.xls,.pptx and be able to edit them, save and close the said file. edit: latest tried code... <?php // Connects to your Database include "configdb.php"; //Retrieves data from MySQL $data = mysql_query("SELECT * FROM employees") or die(mysql_error()); //Puts it into an array while($info = mysql_fetch_array( $data )) { //Outputs the image and other data //Echo "<img src=localhost/uploadfile/images".$info['photo'] ."> <br>"; Echo "<b>Name:</b> ".$info['name'] . "<br> "; Echo "<b>Email:</b> ".$info['email'] . " <br>"; Echo "<b>Phone:</b> ".$info['phone'] . " <hr>"; //$file=fopen("uploadfile/images/".$info['photo'],"r+"); $file=fopen("Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt","r") or exit("unable to open file");; } ?> i am getting the error: Warning: fopen(Applications/XAMPP/xamppfiles/htdocs/uploadfile/images/file.odt): failed to open stream: No such file or directory in /Applications/XAMPP/xamppfiles/htdocs/uploadfile/view.php on line 17 unable to open file the file is in that folder, i don't know it wont find it.

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  • Filter jquery split list

    - by Jason
    see: http://jasondaydesign.com/index2.html I am using easylistsplitter.js to layout the portfolio items. Unfortunately, my filter does not work on all of the items. It only filters the first column. Thoughts? Thanks!

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  • Merging list problem

    - by Martin Malmstrøm
    Sorry about the bad heading, but the question was not easy to compress into one sentence... I have two lists of contigs (list1 and list2). They contain mostly unique contigs, but with some overlap. I want to compare list1 and list2 and then create a list3 that contains all contigs in list1 minus those also present in list2. Is this possible with a simple cat/paste/grep/sort/uniq kind of batch command? Thanks!

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  • Copied a file with winscp; only winscp can see it

    - by nilbus
    I recently copied a 25.5GB file from another machine using WinSCP. I copied it to C:\beth.tar.gz, and WinSCP can still see the file. However no other app (including Explorer) can see the file. What might cause this, and how can I fix it? The details that might or might not matter WinSCP shows the size of the file (C:\beth.tar.gz) correctly as 27,460,124,080 bytes, which matches the filesize on the remote host Neither explorer, cmd (command line prompt w/ dir C:\), the 7Zip archive program, nor any other File Open dialog can see the beth.tar.gz file under C:\ I have configured Explorer to show hidden files I can move the file to other directories using WinSCP If I try to move the file to Users/, UAC prompts me for administrative rights, which I grant, and I get this error: Could not find this item The item is no longer located in C:\ When I try to transfer the file back to the remote host in a new directory, the transfer starts successfully and transfers data The transfer had about 30 minutes remaining when I left it for the night The morning after the file transfer, I was greeted with a message saying that the connection to the server had been lost. I don't think this is relevant, since I did not tell it to disconnect after the file was done transferring, and it likely disconnected after the file transfer finished. I'm using an old version of WinSCP - v4.1.8 from 2008 I can view the file properties in WinSCP: Type of file: 7zip (.gz) Location: C:\ Attributes: none (Ready-only, Hidden, Archive, or Ready for indexing) Security: SYSTEM, my user, and Administrators group have full permissions - everything other than "special permissions" is checked under Allow for all 3 users/groups (my user, Administrators, SYSTEM) What's going on?!

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  • removing items from a generic List<t>

    - by frosty
    I have the following method, I wish to remove items from my collection that match the product Id. Seems fairly straight forward, but i get an exception. Basically my collection is getting out of sync. So what is the best way to remove an item from a collection. public void RemoveOrderItem(Model.Order currentOrder, int productId) { foreach (var orderItem in currentOrder.OrderItems) { if (orderItem.Product.Id == productId) { currentOrder.OrderItems.Remove(orderItem); } } } Exception Details: System.InvalidOperationException: Collection was modified; enumeration operation may not execute

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  • C++, Ifstream opens local file but not file on HTTP Server

    - by fammi
    Hi, I am using ifstream to open a file and then read from it. My program works fine when i give location of the local file on my system. for eg /root/Desktop/abc.xxx works fine But once the location is on the http server the file fails to open. for eg http://192.168.0.10/abc.xxx fails to open. Is there any alternate for ifstream when using a URL address? thanks. part of the code where having problem: bool readTillEof = (endIndex == -1) ? true : false; // Open the file in binary mode and seek to the end to determine file size ifstream file ( fileName.c_str ( ), ios::in|ios::ate|ios::binary ); if ( file.is_open ( ) ) { long size = (long) file.tellg ( ); long numBytesRead; if ( readTillEof ) { numBytesRead = size - startIndex; } else { numBytesRead = endIndex - startIndex + 1; } // Allocate a new buffer ptr to read in the file data BufferSptr buf (new Buffer ( numBytesRead ) ); mpStreamingClientEngine->SetResponseBuffer ( nextRequest, buf ); // Seek to the start index of the byte range // and read the data file.seekg ( startIndex, ios::beg ); file.read ( (char *)buf->GetData(), numBytesRead ); // Pass on the data to the SCE // and signal completion of request mpStreamingClientEngine->HandleDataReceived( nextRequest, numBytesRead); mpStreamingClientEngine->MarkRequestCompleted( nextRequest ); // Close the file file.close ( ); } else { // Report error to the Streaming Client Engine // as unable to open file AHS_ERROR ( ConnectionManager, " Error while opening file \"%s\"\n", fileName.c_str ( ) ); mpStreamingClientEngine->HandleRequestFailed( nextRequest, CONNECTION_FAILED ); } }

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  • How do I open a file in such a way that if the file doesn't exist it will be created and opened automatically?

    - by snakile
    Here's how I open a file for writing+ : if( fopen_s( &f, fileName, "w+" ) !=0 ) { printf("Open file failed\n"); return; } fprintf_s(f, "content"); If the file doesn't exist the open operation fails. What's the right way to fopen if I want to create the file automatically if the file doesn't already exist? EDIT: If the file does exist, I would like fprintf to overwrite the file, not to append to it.

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  • Yet another list comprehension question

    - by relima
    I had this: if Setting["Language"] == "en": f.m_radioBox3.SetSelection(0) elif Setting["Language"] == "pt": f.m_radioBox3.SetSelection(1) elif Setting["Language"] == "fr": f.m_radioBox3.SetSelection(2) elif Setting["Language"] == "es": f.m_radioBox3.SetSelection(3) Then I did this: Linguas = ["en","pt","fr","es"] a = 0 for i in Linguas: if i == Setting["Language"]: f.m_radioBox3.SetSelection(a) a += 1 Is it possible to further simplify this and make it into a one-liner?

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