Hi Nathalie,
On Mon, Jun 6, 2011 at 19:29, Nathalie Conte wrote:
> I need to remove the first 52 bp sequences reads in a fastq file,sequence is
> on line 2.
> fastq file from wikipedia:A FASTQ file normally uses four lines per
> sequence. Line 1 begins with a '@' character and is followed by a s
On Mon, Jun 6, 2011 at 12:29 PM, Nathalie Conte wrote:
> Hi,
>
> I need to remove the first 52 bp sequences reads in a fastq file,sequence
> is on line 2.
> fastq file from wikipedia:A FASTQ file normally uses four lines per
> sequence. Line 1 begins with a '@' character and is followed by a sequ
Hi,
I need to remove the first 52 bp sequences reads in a fastq
file,sequence is on line 2.
fastq file from wikipedia:A FASTQ file normally uses four lines per
sequence. Line 1 begins with a '@' character and is followed by a
sequence identifier and an /optional/ description. Line 2 is the raw
Hello list
I just attempted to upgrade my Catalyst modules and from 3 modules to
upgrade only Catalyst::Runtime failed with this error msg.
>Your installer Makefile.PL has a modification time in the future (1273266119 >
>1273142317).
>
>This is known to create infinite loops in
On Thu, 22 Jan 2009 06:21:32 -0800 (PST)
melbou...@gmail.com wrote:
> I have a Perl script that I run and the out come as showing below:
>
> Reading: server 1\08121100.mls
> Log chain 2:
> Reading: server 2\08120700.mls
> Reading: server 2\08120900.mls
> Reading: server 2\08121100.mls
> L
I have a Perl script that I run and the out come as showing below:
Reading: server 1\08121100.mls
Log chain 2:
Reading: server 2\08120700.mls
Reading: server 2\08120900.mls
Reading: server 2\08121100.mls
Log chain 3:
Reading: server 3\08120700.mls
Reading: server 3\08120900.mls
Readi
From: "Chas. Owens" <[EMAIL PROTECTED]>
> Yes, but I am the one making pronouncements about how people should
> code. Rob was just calling me on being a little pompous. I still
> think that use of $_ in places other than the start of a loop (with a
> function that uses the default variable like s
On Thursday 13 December 2007 03:52, Jenda Krynicky wrote:
>
> From: John W.Krahn <[EMAIL PROTECTED]>
>
> > On Wednesday 12 December 2007 07:15, Jenda Krynicky wrote:
> > > From: jeff pang <[EMAIL PROTECTED]>
> > > >
> > > > You can add a "\n" (or "\r\n" on windows,etc) at the end of
> > > > each el
From: John W.Krahn <[EMAIL PROTECTED]>
> On Wednesday 12 December 2007 07:15, Jenda Krynicky wrote:
> > From: jeff pang <[EMAIL PROTECTED]>
> >
> > > --- "Sayed, Irfan (Irfan)" <[EMAIL PROTECTED]> wrote:
> > > > My query is that can i store the output of this for loop in
> > > > variable or
> > > >
On Dec 13, 2007 1:02 AM, Steve Bertrand <[EMAIL PROTECTED]> wrote:
> Rob Dixon wrote:
> > Chas. Owens wrote:
> >>
> >> Only use the default variable with functions and operators that use
> >> it by default like chomp and regexes.
> >
> > What's this? The Gospel according to Chas?!
>
> Hey now...
>
Rob Dixon wrote:
> Chas. Owens wrote:
>>
>> Only use the default variable with functions and operators that use
>> it by default like chomp and regexes.
>
> What's this? The Gospel according to Chas?!
Hey now...
Take into consideration that this is not everyone's point of view.
Just because you
Chas. Owens wrote:
>
Only use the default variable with functions and operators that use
> it by default like chomp and regexes.
What's this? The Gospel according to Chas?!
Rob
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Chas. Owens wrote:
>
On Dec 12, 2007 1:00 AM, jeff pang <[EMAIL PROTECTED]> wrote:
snip
You can add a "\n" (or "\r\n" on windows,etc) at the end of each
element in the array,like,
snip
In Perl, "\n" is not linefeed, it is the newline character. It
translates to the proper sequence of characte
On Wednesday 12 December 2007 07:15, Jenda Krynicky wrote:
> From: jeff pang <[EMAIL PROTECTED]>
>
> > --- "Sayed, Irfan (Irfan)" <[EMAIL PROTECTED]> wrote:
> > > My query is that can i store the output of this for loop in
> > > variable or
> > > list. so that if i print the content of that variabl
From: jeff pang <[EMAIL PROTECTED]>
> --- "Sayed, Irfan (Irfan)" <[EMAIL PROTECTED]> wrote:
> >
> > My query is that can i store the output of this for loop in
> > variable or
> > list. so that if i print the content of that variable or array then
> > it
> > should print as
> >
> > dadsad
> > as
On Dec 12, 2007 12:04 AM, Sayed, Irfan (Irfan) <[EMAIL PROTECTED]> wrote:
> Hi All,
>
> I have some string stored in array as follows.
>
> @array=(dadsad,assasd) Now if i print this array then it is printing as
> dadsad,assasd
I certainly hope you are not using barewords like this. This will
work
On Dec 12, 2007 1:00 AM, jeff pang <[EMAIL PROTECTED]> wrote:
snip
> You can add a "\n" (or "\r\n" on windows,etc) at the end of each
> element in the array,like,
snip
In Perl, "\n" is not linefeed, it is the newline character. It
translates to the proper sequence of characters on each operating
Irfan, this will work:
#!/opt/local/bin/perl
use warnings;
use strict;
my @output = ("dadsad", "assasd");
foreach (@output)
{
print "$_\n";
}
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--- "Sayed, Irfan (Irfan)" <[EMAIL PROTECTED]> wrote:
>
> My query is that can i store the output of this for loop in
> variable or
> list. so that if i print the content of that variable or array then
> it
> should print as
>
> dadsad
> assasd
>
You can add a "\n" (or "\r\n" on windows,etc)
The built in join() function sounds like what you want.
Read up on it here:
http://perldoc.perl.org/functions/join.html
$output = join("\n", @array);
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Hi All,
I have some string stored in array as follows.
@array=(dadsad,assasd) Now if i print this array then it is printing as
dadsad,assasd
Now i want output like
dadsad
assasd
so i did
for (@array) {
print $_,"\n";
}
My query is that can i store the output of this for loop in vari
From: "Mr. Shawn H. Corey" <[EMAIL PROTECTED]>
> Ken Foskey wrote:
> > I always make that mistake 'if( $a = 10 ) {' that is why I always 'use
> > warnings' and, most importantly, correct the code. Pet peeve is 'use
> > warnings' and then not cleaning them up.
> >
>
> That's because way back in g
Ken Foskey wrote:
Thanks all,
I did read that about for loops somewhere new there was something. I
wonder how many times I have corrupted stuff with the expectation of
having a copy?*
I always make that mistake 'if( $a = 10 ) {' that is why I always 'use
warnings' and, most importantly, correc
Ken Foskey wrote:
I always make that mistake 'if( $a = 10 ) {' that is why I always 'use
warnings' and, most importantly, correct the code. Pet peeve is 'use
warnings' and then not cleaning them up.
That's because way back in grade school, you were taught that 'a = 10' (make a
equal to ten)
Thanks all,
I did read that about for loops somewhere new there was something. I
wonder how many times I have corrupted stuff with the expectation of
having a copy?*
I always make that mistake 'if( $a = 10 ) {' that is why I always 'use
warnings' and, most importantly, correct the code. Pet peev
On Aug 20, 11:51 am, [EMAIL PROTECTED] (Gunnar Hjalmarsson) wrote:
> Paul Lalli wrote:
> > $array[0] = substr( $_, 256, 6 );
> > {
> >no warnings 'numeric';
>
> That would better be:
>
> no warnings qw/numeric uninitialized/;
>
> to cover undefined array elements.
>
> >printf "%06d", $
Paul Lalli wrote:
On Aug 20, 10:47 am, [EMAIL PROTECTED] (Ken Foskey) wrote:
Is there a 'better' way to do this.
Well, if you're sure you know what you're doing, you could just turn
the warning off in the specific scope where you don't want it. I
mean, it's a warning. If you're comfortable w
Ken Foskey wrote:
I have a piece of code that I am assured works and I cannot see why it
would. Code is supposed to force undefined, zero and all space to
numeric zero to stop printf being undefined.
foreach my $value (@array) {
if( ! $value or $value = " " ) {
---
On Aug 20, 10:47 am, [EMAIL PROTECTED] (Ken Foskey) wrote:
> I have a piece of code that I am assured works
Assured by whom?
> and I cannot see why it would.
It doesn't.
> Code is supposed to force undefined, zero and all space to
> numeric zero to stop printf being undefined.
>
> foreach my
- Original Message -
From: "Ken Foskey" <[EMAIL PROTECTED]>
Newsgroups: perl.beginners
To: "beginners perl"
Sent: Monday, August 20, 2007 10:47 AM
Subject: modification
I have a piece of code that I am assured works and I cannot see why it
would.
On 8/20/07, Ken Foskey <[EMAIL PROTECTED]> wrote:
>
> I have a piece of code that I am assured works and I cannot see why it
> would. Code is supposed to force undefined, zero and all space to
> numeric zero to stop printf being undefined.
>
> foreach my $value (@array) {
> if( ! $value or $va
On Tue, Aug 21, 2007 at 12:47:22AM +1000, Ken Foskey wrote:
> I have a piece of code that I am assured works and I cannot see why it
> would. Code is supposed to force undefined, zero and all space to
> numeric zero to stop printf being undefined.
>
> foreach my $value (@array) {
> if( ! $va
I have a piece of code that I am assured works and I cannot see why it
would. Code is supposed to force undefined, zero and all space to
numeric zero to stop printf being undefined.
foreach my $value (@array) {
if( ! $value or $value = " " ) {
$value = 0;
}
}
Will this actu
On 8/16/07, Sayed, Irfan (Irfan) <[EMAIL PROTECTED]> wrote:
> Thanks Chas but my req. is little bit different.
>
> As I said the data in the array will not be fixed so I don't know how
> many elements are present in the array. I don't want to just print the
> contents of the array but to use the co
on then my programme should pick up the
third element of the array
Please help
Regards
Irfan.
-Original Message-
From: Chas Owens [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 16, 2007 4:16 PM
To: Sayed, Irfan (Irfan)
Cc: beginners@perl.org
Subject: Re: Array modification
On 8/16
On 8/16/07, Sayed, Irfan (Irfan) <[EMAIL PROTECTED]> wrote:
> Hi All,
>
> I have one array which stores some data after executing specific
> command. Depends on situation , command has different output at
> different time. sometime array may store 4 values or it may store 5
> values.
>
> Now my req
On Aug 16, 2007, at 11:47 AM, Sayed, Irfan (Irfan) wrote:
I have one array which stores some data after executing specific
command. Depends on situation , command has different output at
different time. sometime array may store 4 values or it may store 5
values.
Now my req. is that I need to as
Hi All,
I have one array which stores some data after executing specific
command. Depends on situation , command has different output at
different time. sometime array may store 4 values or it may store 5
values.
Now my req. is that I need to assign no. to those values.
for example:
if arra
Nath, Alok (STSD) am Dienstag, 18. Juli 2006 15:30:
> Hi,
> In my current program I am not sure where to
> use rowSpan so that I create table like below.
> In otherwords, I want switch 1 to appear
> once only for the two rows.
>
> My main constraint is I dont want to change the program
> style to c
Nath, Alok (STSD) wrote:
Hi,
In my current program I am not sure where to
use rowSpan so that I create table like below.
In otherwords, I want switch 1 to appear
once only for the two rows.
My main constraint is I dont want to change the program
style to create such a table .
Any help will
Hi,
In my current program I am not sure where to
use rowSpan so that I create table like below.
In otherwords, I want switch 1 to appear
once only for the two rows.
My main constraint is I dont want to change the program
style to create such a table .
Any help will be greatly appreciated.
|--
[EMAIL PROTECTED] wrote:
#!/usr/bin/perl -w
use strict;
#use diagnostics;
my $dir = "testdir";
opendir (DH, "$dir") || die "Could not open $dir: $!\n";
my @files; my $keep = 7;
while (defined(my $file = readdir(DH))){
next if $file =~ /^\.+$/;
push (@files, $file);
}
# Skip the rest if numb
#!/usr/bin/perl -w
use strict;
#use diagnostics;
my $dir = "testdir";
opendir (DH, "$dir") || die "Could not open $dir: $!\n";
my @files; my $keep = 7;
while (defined(my $file = readdir(DH))){
next if $file =~ /^\.+$/;
push (@files, $file);
}
# Skip the rest if number of files isn't abo
Babale Fongo wrote:
It was just an attempt to see how someone else may tackle this issue. I
thought of sorting, but I wasn't sure it will do exactly what I expect.
Here is what I've have so far:
my $dir = "/mydir";
opendir(DH, "$dir") || die "Failed to open $dir: $!\n";
my $counter = 0;
while (def
Please bottom post
Babale Fongo wrote:
It was just an attempt to see how someone else may tackle this issue. I
thought of sorting, but I wasn't sure it will do exactly what I expect.
Here is what I've have so far:
my $dir = "/mydir";
opendir(DH, "$dir") || die "Failed to open $dir: $!\n";
my $
sage-
||From: Wiggins d'Anconia [mailto:[EMAIL PROTECTED]
||Sent: Saturday, February 12, 2005 5:19 PM
||To: [EMAIL PROTECTED]
||Cc: beginners@perl.org
||Subject: Re: Compare file modification time
||
||[EMAIL PROTECTED] wrote:
||> How do I best compare mtime of several files. I have
[EMAIL PROTECTED] wrote:
How do I best compare mtime of several files. I have a script for making
daily backups into a given directory. Now I want to modify it to
delete old backups if the total exceed cetain number.
The idea was to compare the mtime of all file to figure out old files to
delete
How do I best compare mtime of several files. I have a script for making
daily backups into a given directory. Now I want to modify it to
delete old backups if the total exceed cetain number.
The idea was to compare the mtime of all file to figure out old files to
delete, but somehow I think it
On 8/19/2004 7:40 PM, Subrata k Bose wrote:
It is extremely inapropriate to CC questions to so many people who are
already members of the mailing list. If you have a question, simply post
it to the list.
Regards,
Randy.
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On May 19, 2004, at 7:21 PM, meb wrote:
My regex looks something like this:
(Save 1st 20 words):
/^(\w|\W){20}/g
^ matches only at the beginning of the string while the /g modifier
tries to create a global search matching all occurrences. Matching all
of what can only be in one place is pointles
On Thu, 2004-05-20 at 01:21, meb wrote:
> Maybe this is because I'm a newbie, or maybe it's because I'm trying to
> modify RSS text. This is a perl script for a web site.
>
> In any case, there's a feed that includes the author at the end of the
> (looong) description. I'd like to limit the decsri
Maybe this is because I'm a newbie, or maybe it's because I'm trying to
modify RSS text. This is a perl script for a web site.
In any case, there's a feed that includes the author at the end of the
(looong) description. I'd like to limit the decsription to the first 20
words, add an ellipsis (...)
--Jerry Maguire
Oracle Certified Professional
Supervisor of Network Operations
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Saturday, March 20, 2004 8:59 AM
To: [EMAIL PROTECTED]
Subject: modification and inode change times
All,
was hoping to get some ide
All,
was hoping to get some ideas on what to use to get all, if any files have
been modified and if so give the file names and dates for these changed
files? If any files were modified more than once then I need to output
the filenames and the date/time as well for that n amount of times.
Stephan Hochhaus wrote:
> Hello list,
>
> I tried to dig my way through my newly acquired Perl ina nutshell and
> Learning Perl, but I couldn't find a satisfying solution to my
> problem:
>
> How can I print the last modification date of a file? It should work
> o
Hello list,
I tried to dig my way through my newly acquired Perl ina nutshell and
Learning Perl, but I couldn't find a satisfying solution to my problem:
How can I print the last modification date of a file? It should work on
different systems (*nix and OS X, Win32 is nice to have but
On Oct 16, Rajat Garg said:
>($1, $2) = split(/=/,$i);
You can't assign to the $ variables. Choose different variable
names.
--
Jeff "japhy" Pinyan [EMAIL PROTECTED] http://www.pobox.com/~japhy/
RPI Acacia brother #734 http://www.perlmonks.org/ http://www.cpan.org/
what does y//
Hi ,
I am getting this error. Kindly help.
The file is having 777 permissions.
$LANGUAG = "/etc/sysconfig/i18n";
open (LNG, "$LANGUAG") || die("Cannot open file /etc/sysconfig/i18n");
@langfile = ;
foreach $i (@langfile)
{
($1, $2) = split(/=/,$i);
print $1;
print $2;
}
close(LNG);
Regards,
Ra
E,$DRVPHONE,$DRVTRKID,$DRVLEASEOP) =
> split(/,/,$_); ...
>}
> }
>
> the "while(){" line returns this message:
>
> Modification of a read-only value attempted
Your outer foreach() loop uses $_ as the loop variable. Inside the loop, $_
is an alias for the value being
t;;
>system "rcp orion:/u1/syncdata/drvdat.$co_id
> /tmp/drv.temp" || next;
>
>open(InFile, "/tmp/drv.temp") || die "No such file: $!\n";
> while(){ chomp;
> my ($DRVID,$DRVNAME,$DRVPHONE,$DRVTRKID,$DRVLEASEOP) =
> split
p" || next;
open(InFile, "/tmp/drv.temp") || die "No such file: $!\n";
while(){
chomp;
my ($DRVID,$DRVNAME,$DRVPHONE,$DRVTRKID,$DRVLEASEOP) = split(/,/,$_);
...
}
}
the "while(){" line returns this message:
Modification of a read-only va
The definition of a hash requires that all keys are unique. To use a
hash the way you want, you may need to make the value for the key
"Acorn Drive" a pointer to an array containing the data you intend [A,
B, ...]. You can use an "anonymous" array to hold the data you want.
(This is what the
If I understand correctly what you are trying to do can't be done with "normal"
hashes. Normally a hash can contain only one value for each unique key, and therefore
you overwrite the value each time you assign a value to a particular key. So you have
two obvious options (in other words that I
-Original Message-
From: Ben Crane [mailto:[EMAIL PROTECTED]]
Sent: Monday, December 02, 2002 4:39 AM
To: [EMAIL PROTECTED]
Subject: modification on hashes/unique values
Hi,
a slight change to the previous mail: if I've got a
key (e.g. A, and I have 3 or 4 keys (which are all A)
which corres
Hi,
a slight change to the previous mail: if I've got a
key (e.g. A, and I have 3 or 4 keys (which are all A)
which correspond to different data...
e.g. Acorn Drive is a key, but there are several parts
the make up Acorn Drive...I want a key (Acorn drive)
to be able to refer to EVERY part of it..
-
From: "Ben Crane" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Friday, November 22, 2002 4:27 PM
Subject: modification of stat problem
> Hi,
>
> Sorry, I forgot to add this:
>
> using file::find::name...what happens with folders
> that have a spac
Hi,
Sorry, I forgot to add this:
using file::find::name...what happens with folders
that have a space in them, e.g. f:\special
information\?
Is there a special way of dealing with that?
Ben
__
Do you Yahoo!?
Yahoo! Mail Plus Powerful. Affordabl
Schwedler Kofoed wrote:
>
> Hi There,
Hello,
> I would like to change a array @xx looking like this:
>
> R23 4587 4985934 3245324 6
>
> to:
>
> R23 4587 4985934 3245324 6
>
> with other words I would like to insert (not replace) at character
> position 8 and 31. I have h
.--[ Schwedler Kofoed wrote (2002/10/22 at 20:25:01) ]--
|
| Hi There,
|
| I would like to change a array @xx looking like this:
|
| R23 4587 4985934 3245324 6
|
| to:
|
| R23 4587 4985934 3245324 6
|
| with other words I would like to insert (n
Hi There,
I would like to change a array @xx looking like this:
R23 4587 4985934 3245324 6
to:
R23 4587 4985934 3245324 6
with other words I would like to insert (not replace) at character
position 8 and 31. I have have tried to use splice and substr but since the
changes
> ($filename,$fileExtention)=fileparse($moofile, '\..*');
> open (OUTFILE1, ">$filename_TEMP.LOG");
>
Perl thinks you are trying to access a variable named
$filename_TEMP. What you want to say is
open( OUTFILE1, ">${filename}_TEMP.LOG" );
HTH,
Tanton
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To unsubscribe, e-mail: [EMAIL PROTEC
Henry Wong wrote:
>
> Actually, my code is something like this:
>
> print "\n\n\nPLEASE ENTER REQUIRED .LOG FILE:";
> $file = ;
> chomp ($file);
> open (INFILE1, "$file");
>
> So how can I use the $file variable to be splitted from its *.log and then
> subsequently using it for appending to a "
z "$filename", the filename comes out smoothly. Pls advise?
Regards,
~ HENRY WONG ~
- Original Message -
From: "NYIMI Jose (BMB)" <[EMAIL PROTECTED]>
To: "Henry Wong" <[EMAIL PROTECTED]>; <[EMAIL PROTECTED]>
Sent: Monday, S
On Mon, 23 Sep 2002, Henry Wong wrote:
> Actually, my code is something like this:
>
> print "\n\n\nPLEASE ENTER REQUIRED .LOG FILE:";
> $file = ;
> chomp ($file);
> open (INFILE1, "$file");
>
> So how can I use the $file variable to be splitted from its *.log and then
> subsequently using it f
Give a look to File::Basename module.
http://search.cpan.org/author/JHI/perl-5.8.0/lib/File/Basename.pm
José.
> -Original Message-
> From: Henry Wong [mailto:[EMAIL PROTECTED]]
> Sent: Monday, September 23, 2002 9:17 AM
> To: [EMAIL PROTECTED]
> Subject: Re: Filena
al Message -
From: "Dharmender Rai" <[EMAIL PROTECTED]>
To: "Henry Wong" <[EMAIL PROTECTED]>; <[EMAIL PROTECTED]>
Sent: Monday, September 23, 2002 2:53 PM
Subject: Re: Filename modification
> Read the name of the file from STDIN. Assign it to
> som
ed to enter a filename. User enters
> REX.log. Program will
> then use the name REX.log for future file
> extension/usage by creating
> various REX files like REX_temp.txt, REX_data.log,
> REX_arranged.log,etc
> ,etc... in other words, how do i make the to
> be dynamic so that
REX_temp.txt, REX_data.log, REX_arranged.log,etc
,etc... in other words, how do i make the to be dynamic so that my
program can use the input filenames for file saving/modification/etc?
Regards,
~ HENRY WONG ~
This e-mail is intended only for the named addressee(s) and may contain confidential
and
At 04:39 AM 8/16/01 -0700, Blair Burns wrote:
>Thanks for your reply, Peter. I think I didn't label
>my packages clearly for you, which likely makes a big
>difference ;-) If this tidbit changes your reply, let
>me know.
Not really. See below.
> > The B in your code uses an X to connect, not A.
Thanks for your reply, Peter. I think I didn't label
my packages clearly for you, which likely makes a big
difference ;-) If this tidbit changes your reply, let
me know. Sorry about this, and thanks again!
> The B in your code uses an X to connect, not A.
> Perhaps you're eliding too
> much inf
At 05:36 AM 8/15/01 -0700, Blair Burns wrote:
>Hi *,
>
>I am rather a beginner to Perl (and programming) but
>am nevertheless faced with maintaining a complex OO
>environment. Yikes! Anyway, here is my problem: I have
>two classes whose constructors return a db handle. "A"
>accepts parameters for
Hi *,
I am rather a beginner to Perl (and programming) but
am nevertheless faced with maintaining a complex OO
environment. Yikes! Anyway, here is my problem: I have
two classes whose constructors return a db handle. "A"
accepts parameters for user/password, while "B",
although it uses A to conne
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