welcome to the monastery vineetha,

more effort you put asking best chances you have to get back a good answer.
You assume (and you are wrong) that every monk will understand your post and the solution is clear for people knowing Perl.
If you think that me or other go on the web to learn what blast, contigs and sequences are just to compose a reply to your question, you are too much optimistic..

Anyway if you can produce some small example, or even better, if you can reduce your problem to something widely understandable, chances are that you'll receive good replies.

if you have some Perl knoweledge the basic structure of your program will be something like: 
##PSEUDOCODE
read from file A
read from file B
process data 
write output to file C

[download]


L*
There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.

In reply to Re: how to create output file using perl by Discipulus
in thread how to create output file using perl by vineetha

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.