parsing script help please
Hi
I have this format of file: (see attached example)
1 3206102-3207048 3411782-3411981 3660632-3661428
2 4481796-4482748 4483180-4483486
and I would like to change it to this
1 3206102-3207048
1 3411782-3411981
1 3660632-3661428
2 4481796-4482748
2 4483180-4483486 .
I have tried with this script to create an array for each line, and to
print the first element (1 or 2) with the rest of the line but the
output don't seem to be right, could you please advise?
#!/software/bin/perl
use warnings;
use strict;
my $file="example.txt";
my $in;
open( $in , '<' , $file ) or die( $! );
#open( $out, ">>txtout");
while (<$in>){
next if /^#/;
my @lines=split(/\t/);
chomp;
for (@lines) { print $lines[0],"\t",$_,"\n"; };
ouput
1 1 i don't want this
1 3206102-3207048
1 3411782-3411981
1 3660632-3661428
1 i don't want this
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4334680-4340171
1 4341990-4342161
1 4342282-4342905
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4481796-4482748
1 4483180-4483486
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4797994-4798062
1 4798535-4798566
1 4818664-4818729
1 4820348-4820395
1 4822391-4822461
1 4827081-4827154
1 4829467-4829568
1 4831036-4831212
1 4835043-4835096
many thanks
Nathalie
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
1 3206102-3207048 3411782-3411981 3660632-3661428
1 4334680-4340171 4341990-4342161 4342282-4342905
1 4481796-4482748 4483180-4483486
1 4797994-4798062 4798535-4798566 4818664-4818729 4820348-4820395
4822391-4822461 4827081-4827154 4829467-4829568 4831036-4831212 4835043-4835096
1 4900554-4900742 4902394-4902628 4906977-4907060 4913927-4914069
5009391-5009459
1 5074531-5074643 5079089-5079191 5083443-5083532 5085695-5085808
5088109-5088213 5091150-5091203 5107470-5107567 5114357-5114549 5123164-5123342
5125892-5126017 5133830-5133931 5140028-5140141 5152185-5152245
1 5579129-5579385 5588670-5589022 5592332-5592864
1 6758978-6759032 6761024-6761054 6785466-6785656 6792400-6793185
6797623-6797757 6799357-6799447 6800654-6800758 6807683-6807876 6810014-6810225
6817856-6818101 6823643-6823758 6832219-6832281 6832953-6833021 6834201-6834263
6834371-6834451 6835651-6835872 6838987-6839075 6845449-6845552 6847380-6847523
6848540-6848680
1 9535604-9536701
1 9538173-9538231 9539987-9540024 9541797-9541837 9543003-9543056
9543398-9543552 9543703-9543899 9545618-9545695 9547080-9547185 9548213-9548365
9550189-9550287 9553589-9553667 9553877-9553973 9556861-9557018 9566271-9566354
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Re: parsing script help please
On Thu, May 31, 2012 at 11:37 AM, nathalie wrote:
>
>
> Hi
> I have this format of file: (see attached example)
> 1 3206102-3207048 3411782-3411981 3660632-3661428
> 2 4481796-4482748 4483180-4483486
>
>
> and I would like to change it to this
> 1 3206102-3207048
> 1 3411782-3411981
> 1 3660632-3661428
> 2 4481796-4482748
> 2 4483180-4483486 .
>
>
> I have tried with this script to create an array for each line, and to
> print the first element (1 or 2) with the rest of the line but the output
> don't seem to be right, could you please advise?
> #!/software/bin/perl
> use warnings;
> use strict;
> my $file="example.txt";
> my $in;
> open( $in , '<' , $file ) or die( $! );
> #open( $out, ">>txtout");
>
>
> while (<$in>){
>next if /^#/;
>my @lines=split(/\t/);
>chomp;
> for (@lines) { print $lines[0],"\t",$_,"\n"; };
>
>
> ouput
> 1 1 i don't want this
> 1 3206102-3207048
> 1 3411782-3411981
> 1 3660632-3661428
> 1 i don't want this
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
>
> 1 1
> 1 4334680-4340171
> 1 4341990-4342161
> 1 4342282-4342905
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
>
> 1 1
> 1 4481796-4482748
> 1 4483180-4483486
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> 1
>
> 1 1
> 1 4797994-4798062
> 1 4798535-4798566
> 1 4818664-4818729
> 1 4820348-4820395
> 1 4822391-4822461
> 1 4827081-4827154
> 1 4829467-4829568
> 1 4831036-4831212
> 1 4835043-4835096
>
> many thanks
> Nathalie
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
> --
> To unsubscribe, e-mail: beginners-unsubscr...@perl.org
> For additional commands, e-mail: beginners-h...@perl.org
> http://learn.perl.org/
>
>
Hi Nathalie,
Instead of using the split function I would personally go for a regular
expression as it allows for a lot more control over what you want to find.
Here is my solution...
#!/usr/local/bin/perl
use strict;
use warnings;
my $fh;
my %results;
open ( $fh, '<', 'temp.txt' ) or die $!;
while ( <$fh> ) {
chomp;
my $line = $_;
my $rownum = substr($line, 0, 1);
my @othernumbers;
while ( /(\d{7}-\d{7})/g ) {
push ( @othernumbers, $1 );
}
$results{$rownum} = \@othernumbers;
}
close $fh;
use Data::Dumper;
print Dumper %results;
This should print the results below:
$VAR1 = '1';
$VAR2 = [
'3206102-3207048',
'3411782-3411981',
'3660632-3661428'
];
$VAR3 = '2';
$VAR4 = [
'4481796-4482748',
'4483180-4483486'
];
And this is I believe where you wanted to go. Of course you could just
print it directly without the need for the temp variables etc but I assume
that you want to do something more with the found values then just dump
them on your screen.
Regards,
Rob
Re: parsing script help please
nathalie wrote:
Hi
Hello,
I have this format of file: (see attached example)
1 3206102-3207048 3411782-3411981 3660632-3661428
2 4481796-4482748 4483180-4483486
and I would like to change it to this
1 3206102-3207048
1 3411782-3411981
1 3660632-3661428
2 4481796-4482748
2 4483180-4483486 .
I have tried with this script to create an array for each line, and to
print the first element (1 or 2) with the rest of the line but the
output don't seem to be right, could you please advise?
#!/software/bin/perl
use warnings;
use strict;
my $file="example.txt";
my $in;
open( $in , '<' , $file ) or die( $! );
#open( $out, ">>txtout");
while (<$in>){
next if /^#/;
my @lines=split(/\t/);
chomp;
for (@lines) { print $lines[0],"\t",$_,"\n"; };
You want something like this:
#!/software/bin/perl
use warnings;
use strict;
my $file = "example.txt";
open my $in, '<', $file or die "Cannot open '$file' because: $!";
while ( <$in> ) {
next if /^#/;
chomp;
my ( $key, @fields ) = split /\t/;
print map "$key\t$_\n", @fields;
}
__END__
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
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Re: parsing script help please
thanks a lot Rob
I would like an output without the $VAR...
so I did add this after the push function and it is perfect, thanks a
lot again
foreach my $number(@othernumbers){print $rownum,"\t",$elet, "\n";}
#!/usr/local/bin/perl
use strict;
use warnings;
my $fh;
my %results;
open ( $fh, '<', 'temp.txt' ) or die $!;
while ( <$fh> ) {
chomp;
my $line = $_;
my $rownum = substr($line, 0, 1);
my @othernumbers;
while ( /(\d{7}-\d{7})/g ) {
push ( @othernumbers, $1 );
}
$results{$rownum} = \@othernumbers;
}
close $fh;
use Data::Dumper;
print Dumper %results;
This should print the results below:
$VAR1 = '1';
$VAR2 = [
'3206102-3207048',
'3411782-3411981',
'3660632-3661428'
];
$VAR3 = '2';
$VAR4 = [
'4481796-4482748',
'4483180-4483486'
];
And this is I believe where you wanted to go. Of course you could just
print it directly without the need for the temp variables etc but I
assume that you want to do something more with the found values then
just dump them on your screen.
Regards,
Rob
On Thu, May 31, 2012 at 11:37 AM, nathalie > wrote:
Hi
I have this format of file: (see attached example)
1 3206102-3207048 3411782-3411981 3660632-3661428
2 4481796-4482748 4483180-4483486
and I would like to change it to this
1 3206102-3207048
1 3411782-3411981
1 3660632-3661428
2 4481796-4482748
2 4483180-4483486 .
I have tried with this script to create an array for each line,
and to print the first element (1 or 2) with the rest of the line
but the output don't seem to be right, could you please advise?
#!/software/bin/perl
use warnings;
use strict;
my $file="example.txt";
my $in;
open( $in , '<' , $file ) or die( $! );
#open( $out, ">>txtout");
while (<$in>){
next if /^#/;
my @lines=split(/\t/);
chomp;
for (@lines) { print $lines[0],"\t",$_,"\n"; };
ouput
1 1 i don't want this
1 3206102-3207048
1 3411782-3411981
1 3660632-3661428
1 i don't want this
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4334680-4340171
1 4341990-4342161
1 4342282-4342905
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4481796-4482748
1 4483180-4483486
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1 1
1 4797994-4798062
1 4798535-4798566
1 4818664-4818729
1 4820348-4820395
1 4822391-4822461
1 4827081-4827154
1 4829467-4829568
1 4831036-4831212
1 4835043-4835096
many thanks
Nathalie
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose
registered office is 215 Euston Road, London, NW1 2BE.
--
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Hi Nathalie,
Instead of using the split function I would personally go for a
regular expression as it allows for a lot more control over what you
want to find. Here is my solution...
#!/usr/local/bin/perl
use strict;
use warnings;
my $fh;
my %results;
open ( $fh, '<', 'temp.txt' ) or die $!;
while ( <$fh> ) {
chomp;
my $line = $_;
my $rownum = substr($line, 0, 1);
my @othernumbers;
while ( /(\d{7}-\d{7})/g ) {
push ( @othernumbers, $1 );
}
$results{$rownum} = \@othernumbers;
}
close $fh;
use Data::Dumper;
print Dumper %results;
This should print the results below:
$VAR1 = '1';
$VAR2 = [
'3206102-3207048',
'3411782-3411981',
'3660632-3661428'
];
$VAR3 = '2';
$VAR4 = [
'4481796-4482748',
'4483180-4483486'
];
And this is I believe where you wanted to go. Of course you could just
print it directly without the need for the temp variables etc but I
assume that you want to do something more with the found values then
just dump them on your screen.
Regards,
Rob
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Re: parsing script help please
You want something like this:
#!/software/bin/perl
use warnings;
use strict;
my $file = "example.txt";
open my $in, '<', $file or die "Cannot open '$file' because: $!";
while ( <$in> ) {
next if /^#/;
chomp;
my ( $key, @fields ) = split /\t/;
print map "$key\t$_\n", @fields;
}
__END__
John
HI John,
work perfectly thanks
thanks
Nat
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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Regex behavior in command line
Hello,
I'm using the following line in Terminal, on OSX Lion, but I can't seem to
match parentheses '()':
perl -n -e 'print if(/\\(Submit\\)/)' visits/admin_add.ctp
I tried with one backslash in front of each '(' ')' as well to no avail.
If I remove the '\'s and '()' the match is printed like so:
end('Submit');?>
My purpose is to make sure I'm matching the correct lines including the
'()', then to alter the code to perform a search and replace on the
matches). Something like:
perl -p -i.bak -e 's/PATTERN/REPLACE/g' INPUT
Thanks!
Jon
Re: Regex behavior in command line
On 12-05-31 01:23 PM, Jon Forsyth wrote:
Hello,
I'm using the following line in Terminal, on OSX Lion, but I can't seem to
match parentheses '()':
perl -n -e 'print if(/\\(Submit\\)/)' visits/admin_add.ctp
I tried with one backslash in front of each '(' ')' as well to no avail.
If I remove the '\'s and '()' the match is printed like so:
end('Submit');?>
My purpose is to make sure I'm matching the correct lines including the
'()', then to alter the code to perform a search and replace on the
matches). Something like:
perl -p -i.bak -e 's/PATTERN/REPLACE/g' INPUT
Thanks!
Mine works with one backslash:
$ perl -n -e 'print"\t$_" if(/\(Submit\)/)'
Submit
(Submit)
(Submit)
This is a test Submit will not repeat
This is a test (Submit) will repeat
This is a test (Submit) will repeat
^D
--
Just my 0.0002 million dollars worth,
Shawn
Programming is as much about organization and communication
as it is about coding.
_Perl links_
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Bareword and strict subs
I'm getting this error in one of my packages (built by a previous coder):
Bareword "%s" not allowed while "strict subs" in use
In this case the "%s" is attrs. Here's the bit of code it's choking on:
sub insert_shift {
my $self = shift;
my $attrs = @_;
my $m = $self->schema->resultset('Shifts')->new(attrs);
$m->insert;
}
I've googled this error, but what I've found is not very informative. I
have no idea what a Bareword is in the Perl context. Can someone
explain what's going on?
--
Mark Haney
Software Developer/Consultant
AB Emblem
ma...@abemblem.com
Linux marius.homelinux 3.3.7-1.fc16.x86_64 GNU/Linux
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Re: Bareword and strict subs
On 12-05-31 06:28 PM, Mark Haney wrote:
sub insert_shift {
my $self = shift;
my $attrs = @_;
Should this be:
my %attrs = @_;
my $m = $self->schema->resultset('Shifts')->new(attrs);
my $m = $self->schema->resultset('Shifts')->new(%attrs);
$m->insert;
}
--
Just my 0.0002 million dollars worth,
Shawn
Programming is as much about organization and communication
as it is about coding.
_Perl links_
official site : http://www.perl.org/
beginners' help : http://learn.perl.org/faq/beginners.html
advance help: http://perlmonks.org/
documentation : http://perldoc.perl.org/
news: http://perlsphere.net/
repository : http://www.cpan.org/
blog: http://blogs.perl.org/
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RE: Bareword and strict subs
A bareword is an unquoted string appearing in Perl source. Depending on context
it is treated as a sub call or a string (or a filehandle and a few other things
I'd imagine).
Barewords that are not sub calls are generally not permitted under "use strict"
(specifically "use strict 'subs'"), with exceptions such as inside a hash key
or immediately preceding a fat comma '=>'.
In your case, you appear to have omitted the sigil $ before 'attrs' in your
call to 'new'.
See 'perldoc perldata' for more info on barewords and 'perldoc strict' for more
info on what "use strict 'subs' forbids and allows.
Cheers,
Michael
Michael Brader
Senior Software Engineer - Billing
Techops - Softdev
Internode http://www.internode.on.net/
From: Mark Haney [ma...@abemblem.com]
Sent: Friday, 1 June 2012 7:58 AM
To: beginners@perl.org
Subject: Bareword and strict subs
I'm getting this error in one of my packages (built by a previous coder):
> Bareword "%s" not allowed while "strict subs" in use
In this case the "%s" is attrs. Here's the bit of code it's choking on:
sub insert_shift {
my $self = shift;
my $attrs = @_;
my $m = $self->schema->resultset('Shifts')->new(attrs);
$m->insert;
}
I've googled this error, but what I've found is not very informative. I
have no idea what a Bareword is in the Perl context. Can someone
explain what's going on?
--
Mark Haney
Software Developer/Consultant
AB Emblem
ma...@abemblem.com
Linux marius.homelinux 3.3.7-1.fc16.x86_64 GNU/Linux
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suggestion for converting perl data to pdf
This really has nothing to do with Perl, but since Perl is the language I use and I trust you are all bright, helpful and experiences I figured I would give it a shot. I work for a startup that builds an academic and administrative platform for private schools and universities in Mexico. Our code base has over 300K lines of Perl and the software basically does everything related to education. ( www.algebraix.com if you're interested and know spanish :] ) The biggest challenge we have is that each school wants their own custom design for printing grades, tuition statements, receipts and other such documentation. Until now we have been solving this problem with the super-awesome Template-Toolkit and then converting it to PDF with wkhtmltopdf. This works fine but the problem is that we know have two full time employees writing TT templates all day. Each time a new customer signs up we have to do anywhere between 10-50 templates. I need to come up with a solution where customers can create their own reports/designs by themselves. I'm thinking of just biting the bullets and creating a javascript monster with drag drop and 6 trillion switches to customize all the little things customers ask my template developers to do. But before I jump into that huge project, I wanted to see if any of you had encountered this same problem and how you had solved it, ( if there is a solution ). Maybe theres already some cool sofware or library that has most of this functionality . I dont know. Just throwing it out there. I appreciate any input & suggestions, thanks for reading. - Jose from Mexico www.algebraix.com
Re: suggestion for converting perl data to pdf
On 12-05-31 07:31 PM, jbiskofski wrote: I appreciate any input& suggestions, thanks for reading. http://scribus.net/canvas/Scribus -- Just my 0.0002 million dollars worth, Shawn Programming is as much about organization and communication as it is about coding. _Perl links_ official site : http://www.perl.org/ beginners' help : http://learn.perl.org/faq/beginners.html advance help: http://perlmonks.org/ documentation : http://perldoc.perl.org/ news: http://perlsphere.net/ repository : http://www.cpan.org/ blog: http://blogs.perl.org/ regional groups : http://www.pm.org/ -- To unsubscribe, e-mail: beginners-unsubscr...@perl.org For additional commands, e-mail: beginners-h...@perl.org http://learn.perl.org/
Re: Bareword and strict subs
On Thu, May 31, 2012 at 18:35:21 -0400 , Shawn H Corey wrote:
> On 12-05-31 06:28 PM, Mark Haney wrote:
> >sub insert_shift {
> > my $self = shift;
> > my $attrs = @_;
>
> Should this be:
> my %attrs = @_;
As Mark seems to be using DBIx::Class, and the new method on ::ResultSet
classes is defined as taking \%attrs, probably not.
--
Chris Nehren | Coder, Sysadmin, Masochist
Shadowcat Systems Ltd. | http://shadowcat.co.uk/
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Re: Bareword and strict subs
On 12-05-31 08:26 PM, Chris Nehren wrote:
On Thu, May 31, 2012 at 18:35:21 -0400 , Shawn H Corey wrote:
On 12-05-31 06:28 PM, Mark Haney wrote:
sub insert_shift {
my $self = shift;
my $attrs = @_;
Should this be:
my %attrs = @_;
As Mark seems to be using DBIx::Class, and the new method on ::ResultSet
classes is defined as taking \%attrs, probably not.
my $attrs = @_;
This will store the number of elements in the array @_ into $attrs. Why
do that when this is simpler:
$obj->insert_shift( scalar @array );
--
Just my 0.0002 million dollars worth,
Shawn
Programming is as much about organization and communication
as it is about coding.
_Perl links_
official site : http://www.perl.org/
beginners' help : http://learn.perl.org/faq/beginners.html
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Re: Bareword and strict subs
On Thu, May 31, 2012 at 20:36:50 -0400 , Shawn H Corey wrote: > >>Should this be: > >> my %attrs = @_; > > > >As Mark seems to be using DBIx::Class, and the new method on ::ResultSet > >classes is defined as taking \%attrs, probably not. > > > > my $attrs = @_; > > This will store the number of elements in the array @_ into $attrs. > Why do that when this is simpler: > > $obj->insert_shift( scalar @array ); Probably because there's supposed to be () round the $attrs and we both missed it. :) -- Chris Nehren | Coder, Sysadmin, Masochist Shadowcat Systems Ltd. | http://shadowcat.co.uk/ -- To unsubscribe, e-mail: beginners-unsubscr...@perl.org For additional commands, e-mail: beginners-h...@perl.org http://learn.perl.org/
Re: Bareword and strict subs
On 12-05-31 09:00 PM, Chris Nehren wrote: On Thu, May 31, 2012 at 20:36:50 -0400 , Shawn H Corey wrote: Should this be: my %attrs = @_; As Mark seems to be using DBIx::Class, and the new method on ::ResultSet classes is defined as taking \%attrs, probably not. my $attrs = @_; This will store the number of elements in the array @_ into $attrs. Why do that when this is simpler: $obj->insert_shift( scalar @array ); Probably because there's supposed to be () round the $attrs and we both missed it. :) That's why it's better to write it like this: my $attrs = shift @_; -- Just my 0.0002 million dollars worth, Shawn Programming is as much about organization and communication as it is about coding. _Perl links_ official site : http://www.perl.org/ beginners' help : http://learn.perl.org/faq/beginners.html advance help: http://perlmonks.org/ documentation : http://perldoc.perl.org/ news: http://perlsphere.net/ repository : http://www.cpan.org/ blog: http://blogs.perl.org/ regional groups : http://www.pm.org/ -- To unsubscribe, e-mail: beginners-unsubscr...@perl.org For additional commands, e-mail: beginners-h...@perl.org http://learn.perl.org/
