Results 1 to 5 of 5
  1. #1
    Chisco1389 is offline Member
    Join Date
    Apr 2011
    Posts
    1
    Rep Power
    0

    Lightbulb Using Java to filter through data

    Hello i am student at the university of Texas at Tyler where i do miRNA targeting research. I use a program to predict possible mRNA targets.

    Point being the program i use returns a huge amount of data, most of which is useless. What i want to know is how i could make a simple java program to search through the given text file and return a set amount of text after a key word. It needs to go through the entire file and return all the hits.

  2. #2
    doWhile is offline Moderator
    Join Date
    Jul 2010
    Location
    California
    Posts
    1,641
    Rep Power
    7

    Default

    Predicting mRNA targets eh? Sounds fun, but the question you've asked is quite general, and will probably result in a general type of answer (such as this one). Here's a link for how to read files:
    Lesson: Basic I/O (The Java™ Tutorials > Essential Classes)
    and you can use String operations (see the API for the String class) to parse and search strings. If you are looking to truly parse the data in detail, look at
    Lesson: Regular Expressions (The Java™ Tutorials > Essential Classes)
    which may or may not be overkill - hard to say without more information. Not to discourage you from using java, but there's a reason perl is used quite often in bioinformatics - its quick and easy for simple tasks like this.

  3. #3
    JavaHater is offline Senior Member
    Join Date
    Dec 2010
    Posts
    165
    Rep Power
    5

    Default

    Quote Originally Posted by doWhile View Post
    but there's a reason perl is used quite often in bioinformatics - its quick and easy for simple tasks like this.
    there are also other reasons why Perl has lost its appeal when compared to Python or Ruby (part of which is Perl's ugly syntax). There's also bioPython and bioRuby.

  4. #4
    Fubarable's Avatar
    Fubarable is offline Moderator
    Join Date
    Jun 2008
    Posts
    19,315
    Blog Entries
    1
    Rep Power
    26

    Default

    Quote Originally Posted by JavaHater View Post
    There's also bioPython and bioRuby.
    Wow, bioPython -- who'd of thunk? Thanks for showing me something new and interesting!

  5. #5
    doWhile is offline Moderator
    Join Date
    Jul 2010
    Location
    California
    Posts
    1,641
    Rep Power
    7

    Default

    there are also other reasons why Perl has lost its appeal when compared to Python or Ruby (part of which is Perl's ugly syntax). There's also bioPython and bioRuby.
    And there's Biojava, Bioperl, BioPHP... (BioSQL if you want to throw that into the mix as well)...all providing similar functionality (I don't see how they directly help with regards to a simple file parsing task such as this). I won't argue the point of what is the predominant language in bioinformatics and why - my point was its about what one is comfortable with - writing something in java might be overkill if it can be done quicker in another language.
    Last edited by doWhile; 04-18-2011 at 06:23 PM.

Similar Threads

  1. data filter
    By karq in forum Java Servlet
    Replies: 3
    Last Post: 10-07-2010, 06:40 AM
  2. Java ME - filebrowser filter
    By NModern in forum NetBeans
    Replies: 1
    Last Post: 07-16-2010, 12:42 PM
  3. Filter table model by data in specific column
    By ribbs2521 in forum New To Java
    Replies: 9
    Last Post: 10-29-2009, 05:41 AM
  4. Sort and filter in Jtable (java ver 1.5 )
    By itaipee in forum AWT / Swing
    Replies: 3
    Last Post: 04-16-2009, 01:03 PM
  5. web content filter or internet filter
    By sundarjothi in forum Advanced Java
    Replies: 3
    Last Post: 05-15-2008, 12:36 PM

Tags for this Thread

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •