Michael Oldham am Freitag, 23. Juni 2006 18:20:
> Hello again,
Hi Michael again,
> Thanks to everyone for their helpful suggestions. I finally got it to
> work, using the following script. However, it takes about 5 hours to
> run on a fast computer. Using grep (in bash), on the other hand, tak
D. Bolliger wrote:
Michael Oldham am Freitag, 23. Juni 2006 18:20:
[...]
A faster strategy would be:
1. create a lookup hash with the IDs of IDFILE (IDs as keys)
[...]
Doh!
That's right. A hash would be a hundred times faster. Here's the rewrite
of my program to use a hash:
#!/usr/bin/p
Michael Oldham wrote:
Hello again,
Thanks to everyone for their helpful suggestions. I finally got it to
work, using the following script. However, it takes about 5 hours to
run on a fast computer. Using grep (in bash), on the other hand, takes
about 5 minutes (see below if you are interested
Michael Oldham am Freitag, 23. Juni 2006 18:20:
> Hello again,
Hello Michael
> Thanks to everyone for their helpful suggestions. I finally got it to
> work, using the following script. However, it takes about 5 hours to
> run on a fast computer. Using grep (in bash), on the other hand, takes
>
t
done
-Original Message-
From: Muma W. [mailto:[EMAIL PROTECTED]
Sent: Wednesday, June 14, 2006 12:20 AM
To: Beginners List
Subject: Re: A loop to parse a large text file--output is empty!
Michael Oldham wrote:
> Dear all,
>
> I am a Perl newbie struggling to accomplish
[snip]
probe:HG_U95Av2:1138_at:395:301; Interrogation_Position=2631;
...
probe:HG_U95Av2:107_at:543:519; Interrogation_Position=258; Antisense;
...
probe:HG_U95Av2:1156_at:528:483; Interrogation_Position=2054;
...
probe:HG_U95Av2:1102_s_at:541:589; Interrogation_Position=4316;
[snip]
-Original Message-
From: Jenda Krynicky [mailto:[EMAIL PROTECTED]
Sent: Wednesday, June 14, 2006 8:02 AM
To: Timothy Johnson; Michael Oldham; [EMAIL PROTECTED] Org
Subject: RE: A loop to parse a large text file--output is empty!
>> From:"Timothy Johnson" &
Michael Oldham wrote:
Dear all,
I am a Perl newbie struggling to accomplish a conceptually simple
bioinformatics task. I have a single large file containing about
200,000 DNA probe sequences (from an Affymetrix microarray), each of
which is accompanied by a header, like so (this is in FASTA for
On 6/13/06, Michael Oldham <[EMAIL PROTECTED]> wrote:
while () {
print OUT scalar();
You don't want that second use of . Check the documentation
for readline() in the perlfunc manpage. Hope this helps!
--Tom Phoenix
Stonehenge Perl Training
--
To un
PROTECTED]
Sent: Tuesday, June 13, 2006 7:13 PM
To: Timothy Johnson; [EMAIL PROTECTED] Org
Subject: RE: A loop to parse a large text file--output is empty!
Thanks Timothy. I tried the code you supplied and unfortunately the
output file is still empty. Do you think there might be a problem with
the re
ent: Tuesday, June 13, 2006 6:59 PM
To: Michael Oldham; [EMAIL PROTECTED] Org
Subject: RE: A loop to parse a large text file--output is empty!
One problem is that you are using the $_ variable twice.
"while()" assigns $_ to the current line being read, and
"foreach(@array)" as
One problem is that you are using the $_ variable twice.
"while()" assigns $_ to the current line being read, and
"foreach(@array)" assigns $_ to the current element of the array in
question.
It's usually a good idea to be more explicit anyway, and keep the $_
usage to a minimum so you don't hav
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