"Michael S. Robeson II" <[EMAIL PROTECTED]> wrote in message ...
> open(DNA_SEQ, $dna_seq)
Due to precedence, the parens are optional here.
> open(OUTFILE, ">indel_list_"."$dna_seq")
^
">indel_list_$dna_seq" or ">indel_list_".$dna_seq
> foreach (keys
This is a really cool problem. See solution below. Michael, next time post
some code please.
Thanks,
ZO
--
#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;
my(%gap, $animal);
while () {
if (/>(\w+)/) {
$animal = $1;
} else {
while (/(-+)/) {
$gap{$animal
I cleaned up the code a little. So, here it is for anyone interested:
#!usr/bin/perl
# By Michael S. Robeson II with the help from the folks at lernperl.org
and bioperl.org
# 10/16/2004
# Last updated: 10/17/2004
# This script was made for the purpose of searching for indels (gaps)
in aligned
# D
Errin,
Thanks so much! I will spend the weekend going over what you've posted.
Looks like I will learn a lot from this post alone. This stuff is so
addictive. I can spend hours doing this and not realize it. If I am
successful or not is another story! :-)
I'll definitely let you know if I have
On Thu, 14 Oct 2004 16:11:42 -0600, Michael Robeson <[EMAIL PROTECTED]> wrote:
> Yeah, I have just submitted that same question verbatim to the bio-perl
> list. I am still running through some ideas though. I have both
> Bioinformatics perl books. They are not very effective teaching books.
>
> Th
On Thursday 14 October 2004 21:44, Michael Robeson wrote:
> Here is as far as I can get with some real code and pseudo code. This
> is just to show you that I am actually trying. :-)
Hi Michael,
this looks quite promising - I'll try to sketch a solution without giving
everything away ;-)
>
> Ps
Yeah, I have just submitted that same question verbatim to the bio-perl
list. I am still running through some ideas though. I have both
Bioinformatics perl books. They are not very effective teaching books.
The books spend too much time on using modules. Though while I
understand the usefulness
On Thu, Oct 14, 2004 at 04:50:30PM -0500, Errin Larsen wrote:
> Hi Paul,
> I think you missed a critical part of Mike's post!:
No, I didn't miss it. I just thought it likely that Mike could get to
there from where I left off, so I gave a solution to the bit that seemed
most troublesome.
>
On Thu, 14 Oct 2004 23:23:48 +0200, Paul Johnson <[EMAIL PROTECTED]> wrote:
> On Thu, Oct 14, 2004 at 11:02:06AM -0600, Michael Robeson wrote:
>
> > I have a set of data that looks something like the following:
>
> > So, my problem is that I think I know some of the bits of code to put
> > into p
Here is as far as I can get with some real code and pseudo code. This
is just to show you that I am actually trying. :-)
Pseudo - code
# open DNA sequence file
print "Enter in the name of the DNA sequence file:\n";
chomp (my $dna_s
On Thu, Oct 14, 2004 at 11:02:06AM -0600, Michael Robeson wrote:
> I have a set of data that looks something like the following:
> So, my problem is that I think I know some of the bits of code to put
> into place the problem is I am getting lost on how to structure it all
> together.
>
On Thu, 14 Oct 2004 16:08:44 -0400, Willy West <[EMAIL PROTECTED]> wrote:
> On Thu, 14 Oct 2004 14:47:57 -0500, Errin Larsen <[EMAIL PROTECTED]> wrote:
> >
>
> > > bio-informatics is a big area in which Perl is involved... there's even
> > > a book from O'reilly on the subject...
>
> > If what
On Thu, 14 Oct 2004 14:47:57 -0500, Errin Larsen <[EMAIL PROTECTED]> wrote:
>
> > bio-informatics is a big area in which Perl is involved... there's even
> > a book from O'reilly on the subject...
> If what you say is true, then maybe Mike needs to take his questions
> to those list? I mean
On Thu, 14 Oct 2004 15:40:24 -0400, Willy West <[EMAIL PROTECTED]> wrote:
> > PS: is this a common problem/exercise in some class somewhere? I keep
> > seeing requests for help having to do with those exact strings of DNA
> > data. Is there a bunch of people working on DNA projects using Perl
> >
> PS: is this a common problem/exercise in some class somewhere? I keep
> seeing requests for help having to do with those exact strings of DNA
> data. Is there a bunch of people working on DNA projects using Perl
> somewhere? Or, is this some homework?
bio-informatics is a big area in which Pe
On Thu, 14 Oct 2004 11:02:06 -0600, Michael Robeson <[EMAIL PROTECTED]> wrote:
> I have a set of data that looks something like the following:
>
<>
>
> So, any suggestions would be greatly appreciated. If anyone can help me
> out with all or even just bits of this I would greatly appreciate it.
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