No problem Changrong, glad to be of help to a fellow scientist. And thanks
to John and the other for showing much more elegant ways of solving the
problem.
Cheers!
Anjan
On Thu, Dec 2, 2010 at 3:40 AM, John W. Krahn wrote:
> Changrong Ge wrote:
>
>> Hi guys,
>>
>
> Hello,
>
>
> Thanks a lot
Changrong Ge wrote:
Hi guys,
Hello,
Thanks a lot for this issue and with Anjan's help here I got the
wonderful script for my work and I post below, hopefully it would be helpful
for others--works perfectly for fasta file.
Also thanks to others who are interested in the discussion, b
Hi guys,
Thanks a lot for this issue and with Anjan's help here I got the
wonderful script for my work and I post below, hopefully it would be helpful
for others--works perfectly for fasta file.
Also thanks to others who are interested in the discussion, but I think
it takes time for me to
>
> Why are you returning the results of //g to an empty list, in void context?
Forcing list context; //g alone is scalar, which using that regex, it grabs
the first character, executes the code.. And that's it. As a list, it does
what it should do, so to say :)
If you are going to skip whitespac
Brian Fraser wrote:
...and before someone chastises me (rightly so) for using (??{CODE}) in a
situation where a perfectly good (?{CODE}) would've done just fine, or for
not skipping that first line, or using $1 instead of the more scalable $^N..
Here's a little preemptive redemption:
while () {
Brian Fraser wrote:
On Wed, Dec 1, 2010 at 4:58 PM, Mariano Loza Collwrote:
Alternatively, a good samaritan out there can gelp you with a one or
two-liner code.
If you only want to count letters, here's the 1-2 liner code, I guess:
#! /usr/bin/perl
use strict;
use warnings;
use 5.010;
my %let
...and before someone chastises me (rightly so) for using (??{CODE}) in a
situation where a perfectly good (?{CODE}) would've done just fine, or for
not skipping that first line, or using $1 instead of the more scalable $^N..
Here's a little preemptive redemption:
while () {
>next if /^>/;
>
Hi guys,
Thank you so much for the help and I really really appreciate what you
guys did for me.
I will definitely try all your suggestions plus those scripts.
Good to be here and also learn a lot by reading emails on perl
discussion.
Regards,
Changrong
On Wed, Dec 1, 201
On Wed, Dec 1, 2010 at 4:58 PM, Mariano Loza Coll wrote:
Alternatively, a good samaritan out there can gelp you with a one or
two-liner code.
If you only want to count letters, here's the 1-2 liner code, I guess:
> #! /usr/bin/perl
> use strict;
> use warnings;
> use 5.010;
>
> my %letter_count;
On 10-12-01 02:58 PM, Mariano Loza Coll wrote:
gi|61499|emb|CAA24495.1| src [Avian sarcoma virus]
MGSSKSKPKDPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGGFNTSDTV
TSPQRAGALAGGVTTFVALYDYESWIETDLSFKKGERLQIVNNTEGNWWLAHSLTTGQTGYIPSNYVAPS
DSIQAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKG
> here is the script. give it a name, say, seqComp.pl. usage: perl
seqComp.pl
> .
> HTH,
> Anjan
...And as I was writing my reply, Anjan the good samaritan came to the
rescue.
Thanks Anjan!
Mariano
Hello everyone,
I'm so glad that I could finally be of some help to a group that helped me
before.
> Hi Changrong
>
> The problem doesn't seem difficult, but I'm afraid we don't have much
> knowledge of bioinformatics between us. If you post a sample of input
> data and the corresponding output
here is the script. give it a name, say, seqComp.pl. usage: perl seqComp.pl
.
HTH,
Anjan
#! /usr/bin/perl -w
use strict;
open (S, "$ARGV[0]") || die "cannot open FASTA file to read: $!";
my %s;# a hash of arrays, to hold each line of sequence
my %seq; #a hash to hold the AA sequences.
my $key;
On 01/12/2010 08:44, Changrong Ge wrote:
I am quite new to this perl language-I am from biochemistry field.
Now trying to write a script for my current work but could not make
it. The idea is to calculate the composition (percentage) of amino
acids in a protein sequence.
Input is a series of fa
Tack så mycket,
I will check that website
The output is the percentage of each amino acid in the protein.
For example, protein A is 100 amino acid long, in which there are 10
lysine, then the output for lysine is 0.1, the same rule for the
other amino acids.
In t
Tack så mycket, I will check that website.
The values are the percentage of amino acids in the sequence.
For example, protein A is 100 amino acid long, in which there are 12
arginine, then output for arginine is 12%; for the other 19 amino acids,
it is the same rule.
Thanks anyway,
Changrong
Hi,
On Wednesday 01 December 2010 10:44:17 Changrong Ge wrote:
> Hi,
> I am quite new to this perl language-I am from biochemistry field.
> Now trying to write a script for my current work but could not make it.
> The idea is to calculate the composition (percentage) of amino acids in
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