----- Original Message -----
From: "Charles K. Clarkson" <[EMAIL PROTECTED]>
To: "'Öznur Tastan'" <[EMAIL PROTECTED]>; "'Perl Lists'"
<[EMAIL PROTECTED]>
Sent: Tuesday, February 24, 2004 10:56 PM
Subject: RE: how to push a double dimensional array
> Öznur Tastan <[EMAIL PROTECTED]> wrote:
> :
> : ----- Original Message -----
> : From: "Charles K. Clarkson" <[EMAIL PROTECTED]>
> : To: "'Öznur Tastan'" <[EMAIL PROTECTED]>; "'Perl Lists'"
> : <[EMAIL PROTECTED]>
> : Sent: Tuesday, February 24, 2004 8:59 PM
> : Subject: RE: how to push a double dimensional array
> :
> :
> : > Öznur Tastan <[EMAIL PROTECTED]> wrote:
> : > :
> : > :
> : > : Ok: I am starting from the beginning.
> : >
> : > I thought I had accidentally discouraged you.
> : >
> : >
> : > : The alignment is alignment of two strings so that similar
> : > : characters according to a scoring system (this is out of scope
> : > : I think) should be in the same register and there can be gaps
> : > : in one of the strings denotes as a dash.
> : >
> : > What do you mean by "should be in the same register"? What
> : > is a register?
> :
> : Like in the alignment below A is in the same 'register'( bad
> : English himm :) with - but seq1 and seq2 have these information
> : already so when I know seq1 and seq2 I don't need any further
> : information to visualize the alignment.
> : Three feature is enough to define my alignment
> :
> : AADALLL
> : - - EVLLL
> : the alignment is there ( this is pairwise alignment of protein
> : sequences that can be calculated by dynamic programming of two
> : strings)
> You are aware that this is the first time you have actually come
> out and said this was biology related, right?
Yes I know but I didn't want bother you all with details.
After all a protein sequence is a string of characters:)
Have you checked out
> http://bio.perl.org/? I don't know enough about your field to know
> if your current application is already solved there.
Yes I have already checked there.
> Okay, so we have established that each alignment has three
> characteristics and we are trying to see how best to arrange
> the alignments in a data structure that will ease your manipulation
> of those alignments.
>
>
> : > : So my alignments have three features (seq1 seq2 and the score
> : > : of the alignments)
> : > : seq1: AADALLL
> : > : seq2: - - EVLLL
> : > : score:12
> : > :
> : > : There are groups of alignments that I want to keep separated.
> : > : Say I have 15 alignments (the numbers and distributions can
> : > : be changed with different input strings)
> : > : 3 of the alignments belong to first group
> : > : 4 of them second belong to 2nd group.
> : > : 5 of them belong to 3rd
> : > : 2 of them belong to 4th
> : > : 1 of them belong to 5th)
> : >
> : > What is a group of alignments grouped by? Is it by score
> : > or some other quality?
> :
> : No not score some other quality related to origins of the
> : sequences ( again related to biology ).
> : So the alignments of certain sequence pairs should belong to one
> : group and the others another. So we for the scope of problem
> : believe me it is not important.
>
> So, in this example we have 15 alignments and they can be
> grouped by their origin.
>
> Are the group names alphanumeric of numbered? If numbered, are
> they in sequence? Assuming they are not a numbered sequence, I
> would think the top level of your structure would be a hash.
>
>
> (
> group_name_1 => ( '3 alignments' ),
> group_name_2 => ( '4 alignments' ),
> group_name_3 => ( '5 alignments' ),
> group_name_4 => ( '2 alignments' ),
> group_name_5 => ( '1 alignments' ),
> )
>
>
> What goes inside each hash value depends on what you need
> to do with those values. I am still not clear what that is, but
> you have two basic choices:
>
> ( 'AADALLL', '- - EVLLL', 12 )
>
> Or:
>
> (
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> )
>
> A hash of an array of arrays might look like this:
> (
> group_name_1 => [
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> ],
> group_name_2 => [
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> ],
> group_name_3 => [
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> ],
> group_name_4 => [
> [ 'AADALLL', '- - EVLLL', 12 ],
> [ 'AADALLL', '- - EVLLL', 12 ],
> ],
> group_name_5 => [
> [ 'AADALLL', '- - EVLLL', 12 ],
> ],
> )
>
> Of course, the alignments would all be different and the and
> the group names would probably be more topical, but I don't know
> enough biology to make up other values.
>
> Assuming this data structure is named %groups, we access
> each 'seq1' of a group named $group with:
>
> my $group = 'group_name_1';
> foreach my $sequence ( @{ $groups{ $group } } ) {
> print "$sequence->[0]\n";
> # do something with each sequence
> }
>
>
> A hash of array of hashes might look like this:
>
> (
> group_name_1 => [
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> ],
> group_name_2 => [
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> ],
> group_name_3 => [
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> ],
> group_name_4 => [
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> ],
> group_name_4 => [
> {
> seq1 => 'AADALLL',
> seq2 => '- - EVLLL',
> score => 12
> },
> ],
> )
>
>
> Assuming this data structure is named %groups, we access
> each 'seq1' of a group named $group with:
>
> my $group = 'group_name_1';
> foreach my $sequence ( @{ $groups{ $group } } ) {
> print "$sequence->{seq1}\n";
> # do something with each sequence
> }
>
>
> Unfortunately, I have no idea if I have helped or not.
No you exactly helped me but now let me ask one more question.
When using a hash of array of hashes or a hash of an array of arrays
how can I insert an new element in if I know which group it belongs to?
for example how can I insert a new alignment whose
seq1 AAAK
seq2 VVV-
score 10
into group_name_1
without backtracking how many elements group_name_1 contains
so something like "push"?????
thanks A LOT
oznur
> To unsubscribe, e-mail: [EMAIL PROTECTED]
> For additional commands, e-mail: [EMAIL PROTECTED]
> <http://learn.perl.org/> <http://learn.perl.org/first-response>
>
--
To unsubscribe, e-mail: [EMAIL PROTECTED]
For additional commands, e-mail: [EMAIL PROTECTED]
<http://learn.perl.org/> <http://learn.perl.org/first-response>
