A quick-and-dirty method would be to output to an HTML file and use tags:
#begin script
print "<html><head><title>Matches for AGTG</title></head>";
while(<>)
{
#convert input line into regular text, and then...
s/\n/<br>/g;
s:(AGTG):<font color="FF00FF">$1</font>:gi;
print;
}
print "</html>"
#end script
Why make your own custom viewer?
-- Matt
To: [EMAIL PROTECTED],
[EMAIL PROTECTED]
cc: (bcc: Matt B. Grimaldi)
Date: 05/14/2002 07:13 AM
From: [EMAIL PROTECTED]
Subject: Pattern search program
Hi,
as I am relatively new to Perl it would be great if anybody of you could
help me to solve the following problem:
Description of the problem:
- I would like to read a sequence in Fasta Format (stored as text file
on a local hard disk)
e.g
> Test1
AGTGGTGCAGTGCGTCGTTTTTGCAGTCCC.....
- Then I would like to search for a certain pattern within the sequence
(e.g. AGTG).
--> I know how to do that but now comes my question
What modules do I need to graphically display all found patterns within
the queried sequence?
Example for the output on the screen:
>Test1
AGTGGTGCAGTGCGTCGTTTTTGCAGTCCC....
Is there same code (examples) available?
Thanks for your help
Heiko
(See attached file: C.htm)
*******************Internet Email Confidentiality Footer*******************
Privileged/Confidential Information may be contained in this message. If
you are not the addressee indicated in this message (or responsible for
delivery of the message to such person), you may not copy or deliver this
message to anyone. In such case, you should destroy this message and kindly
notify the sender by reply email. Please advise immediately if you or your
employer do not consent to Internet email for messages of this kind.
Opinions, conclusions and other information in this message that do not
relate to the official business of my firm shall be understood as neither
given nor endorsed by it.
|
Hi, as I am relatively new to Perl
it would be great if anybody of you could help me to solve the following
problem: Description of the problem: - I would like to read a
sequence in Fasta Format (stored as text file on a
local hard disk) e.g > Test1 AGTGGTGCAGTGCGTCGTTTTTGCAGTCCC..... - Then I would like to search
for a certain pattern within the sequence (e.g. AGTG). à I know how to do that but now comes
my question What modules do I need to
graphically display all found patterns within the queried sequence? Example for the output on the
screen: >Test1 AGTGGTGCAGTGCGTCGTTTTTGCAGTCCC.... Is there same code (examples)
available? Thanks for your help Heiko |
