I am dinking around with perl for bioinformatics purposes. I have written a
small perl script that reads FASTA formatted sequence files and searches the
sequence therein for user-entered sequences.
This is primarily targetted at protein sequence analysis and for my purposes,
I've included -
Hi
I am in process of creating a template Say a HTML template...pasting one sample line
below.
and there is one text file(config.txt) has several entries
1x1_image=/images/temp_white.gif
topColor=FF
The problem is when I ryun the perl script it has to identify that topColor and
1x1_im
Praedor Atrebates wrote:
> I am dinking around with perl for bioinformatics purposes. I have
> written a small perl script that reads FASTA formatted sequence files
> and searches the sequence therein for user-entered sequences.
>
> This is primarily targetted at protein sequence analysis and for
Praedor Atrebates wrote:
I am dinking around with perl for bioinformatics purposes. I have written a
small perl script that reads FASTA formatted sequence files and searches the
sequence therein for user-entered sequences.
This is primarily targetted at protein sequence analysis and for my p
On Jun 14, Praedor Atrebates said:
$dnakmotif = '[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
I am just learning as I go here but there are two problems with this, one of
which I understand but the other I do not. First, the one I do not
understand. My intent with the value set to $dnakmoti
Anish Kumar K. wrote:
I am in process of creating a template Say a HTML
template...pasting one sample line below.
and there is one text file(config.txt) has several entries
1x1_image=/images/temp_white.gif
topColor=FF
You can store config.txt in a hash and use the s/// operator:
my %tmpl_
On Tuesday 14 June 2005 16:37, Wagner, David --- Senior Programmer Analyst ---
WGO wrote:
[...]
> > I have this (pertinent) code in my script:
> >
> > $dnakmotif ='[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
>
> $dnakmotif ='[KPH](L{3,5}|V{3,5}|I{3,5}|F{3,5}|Y{3,5}|A{3,5}){1,}[KRH]';
> This
On Tuesday 14 June 2005 17:34, Jeff 'japhy' Pinyan wrote:
> On Jun 14, Praedor Atrebates said:
> > $dnakmotif = '[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
> >
> > I am just learning as I go here but there are two problems with this, one
> > of which I understand but the other I do not. First, t
PROTECTED]
Sent: Tuesday, June 14, 2005 4:30 PM
To: Wagner, David --- Senior Programmer Analyst --- WGO; Perl Beginner
Subject: Re: ???UNSURE??? RE: need help with regular expression
[Tim Johnson]
Originally I had thought to assign L, I, V, F, Y, and A to another
variable,
called $hydrophobe or som
On Jun 14, Praedor Atrebates said:
On Tuesday 14 June 2005 17:34, Jeff 'japhy' Pinyan wrote:
The [...] construct is a character class -- it represents a set of
characters, any of which can match. Thus, [KRH] matches a 'K', an 'R', or
an 'H'. But [A{3,}B{3,}] is really just the same as [AB3,{
Programmer Analyst ---
WGO; Perl Beginner
Subject: RE: ???UNSURE??? RE: need help with regular expression
When you say "a series ... 3 to 5 characters in length", do you mean
LLL,III,VVV,FFF,YYY
Or
LIV,FLY,YYL,FFI
Because you could try something like
/[KRH][LIVFY]{3,5}[KRH]/
(not te
On Wednesday 15 June 2005 09:16 am, Sugrue, Sean wrote:
> There is a program called a regular expression coach
> http://www.weitz.de/regex-coach/ which is a big help with difficult
> Expressions.
[...]
Thank you! I'll take a look.
> When you say "a series ... 3 to 5 characters in length", do you
On 6/14/05, Praedor Atrebates <[EMAIL PROTECTED]> wrote:
> On Tuesday 14 June 2005 16:37, Wagner, David --- Senior Programmer Analyst ---
> WGO wrote:
> [...]
> > > I have this (pertinent) code in my script:
> > >
> > > $dnakmotif ='[KRH][L{3,}V{3,}I{3,}F{3,}Y{3,}A{3,}][KRH];
> >
> > $dnakmo
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