how to search for intervals in multiple columns?
hi
i have a dataset consisting of an array of arrays.
$data = [
[q_beg1, q_end1, s_beg1, s_end1]
[q_beg2, q_end2, s_beg2, s_end2]
[q_beg3, q_end3, s_beg3, s_end3]
...
]
q_beg, q_end, s_beg, s_end are all integers.
now, i would like to find all rows where q_beg and q_end are within one
interval (int1_beg, int1_end) while s_beg and s_end are within another
interval (int2_beg, int2_end).
this can be done with grep:
grep {$_-[0] int1_beg and $_-[1] int1_end and
$_-[2] int2_beg and $_-[3] int2_end} @$data;
however, this is too slow for my purpose. so how to speed up such
selection?
the query would be simple enough in a relational database, however i
want to avoid using a database using tables on disk.
i should think this was a pretty generic problem.
ideas are most welcome !
best regards
martin
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can system() interrupt perl at runtime?
Hi Is there a way to make an exception from an external program run with system( program, arg1, arg2, .. ); trigger a perl exception? that is, without explicitly checking $!, $? or $@ after every call ? Martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: how do i list the methods connected to a object?
On Wed, Aug 06, 2003 at 10:24:09PM +0100, Rob Dixon wrote: Martin A. Hansen [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] On Tue, Aug 05, 2003 at 08:18:24PM +0100, Rob Dixon wrote: Ovid [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] --- Peter Scott [EMAIL PROTECTED] wrote: The problem here is that it will not print inherited or AUTOLOADed methods. [snip] So traverse the inheritance hierarchy and do the same thing with each class: http://search.cpan.org/author/SBURKE/Class-ISA-0.32/ISA.pm That's certainly a decent 95% solution and if you *really* need it, it's a good idea. The original problem, though, is not one that I want to encourage most people to solve because for most programmers, when things get that complicated, it turns out that there's an underlying design flaw that needs to be addressed. Of course, people seem to get mad when I say that :) I'll second that. Absolutely. If you've created an object and are asking, 'Now what can I do with this object?' then you're not designing software, you're laying bricks. Find a module that, from the documentation, looks like it will do what you want. Then commit to using that module with the documented interface alone. After that, if you find you've made the wrong decision, be prepared to backtrack as far as necessary to redeem yourself. first of all. objects and modules are for software reuse as i understand it. so installing and using modules from CPAN leaves me as a bricklayer! Being a bricklayer is a fine thing. But I thought this group was for beginner Perl programmers? If you take your module, poke it around a little, and say 'I wonder what this will do if...' then you will probably end up with Carhenge. Read the Owners' Manual and you'll find that you could have driven countless times to visit the magnificent results of a bricklayer at work across the country. hah! so this is the sad story of OO perl. i have been warned off OO perl repeatedly, but using Bio:: (which i believe is as extensive as Net:: and HTTP::) is a major source of software reuse, especially because Bio:: stuff has a lot of parsers of text flatfiles that keep altering format. i was really hoping that someone more clever than i, had this problem solved ... :oP martin Cheers, Rob -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: how do i list the methods connected to a object?
aargh :o) i was hoping there was a simple answer to this. the object im
investigating do apparantly inherets stuff :/
im not into OO perl at all, and i guess this is the reason why.
ok, so the problem is rather complex, but thats just another perl problem then.
and this one must have been solved by others. i have been looking at the
Class::Inspector module on CPAN, which can track the inheritance i think.
ill add my code snippet here to elaborate on the specific problem. and attach a
test file for the parser.
the problem is that the objects $hit and $hsp gives access to a lot of usefull
functions, but what are they???
#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Bio::SearchIO;
my ( $script, $usage, @files, $file );
my ( $searchio, $result, $blast_report, $algorithm_type, $hit, $hit_name, $hsp,
$bit_score,
$query_beg, $query_end, $query_name, $subject_beg, $subject_end, $strand, $eval,
$frame );
$script = ( split /, $0 )[ -1 ];
$usage = qq(
$script by Martin A. Hansen, July 2003.
$script parses blast repport files and writes GFF to STDOUT
Usage: $script blast blast blast
blast - blast report files
);
print $usage and exit if not @ARGV;
@files = @ARGV;
foreach $file ( @files )
{
$searchio = new Bio::SearchIO ( -format = 'blast', -file = $file );
$result = $searchio-next_result;
$query_name = $result-query_name;
$result-database_name;
$algorithm_type = $result-algorithm;
while ( $hit = $result-next_hit )
{
$hit_name= $hit-name;
$hsp = $hit-next_hsp;
$eval= $hsp-evalue;
$bit_score = $hsp-bits;
$strand = $hsp-strand( subject );
$frame = $hsp-frame;
$query_beg = $hsp-query-start;
$query_end = $hsp-query-end;
$subject_beg = $hsp-subject-start;
$subject_end = $hsp-subject-end;
if ( $strand eq 1 ) {
$strand = +;
} elsif ( $strand eq -1 ) {
$strand = -;
} else {
$strand = .;
}
print join( \t,
$hit_name,
$algorithm_type,
similarity,
$subject_beg,
$subject_end,
$bit_score,
$strand,
$frame,
Target \$query_name\ $query_beg $query_end ; E_value $eval
);
print \n;
}
}
On Tue, Aug 05, 2003 at 05:48:04AM -0700, Ovid wrote:
--- Martin A. Hansen [EMAIL PROTECTED] wrote:
hi
i wonder how i can list all the methods availible from a given object?
martin
Hi Martin,
The simple answer: You can't. Welcome to Perl.
The long answer: there are a variety of strategies you can use to try and figure
this out, but
all of them fall short. For example, here's a snippet that prints out defined
subroutines (or
methods) in a given package:
{
no strict 'refs';
my $namespace = sprintf %s::, $CLASS;
foreach (keys %{$namespace}) {
my $test_sub = sprintf %s%s, $namespace, $_;
print $test_sub\n unless defined $test_sub;
}
}
The problem here is that it will not print inherited or AUTOLOADed methods. It
might be
sufficient for your needs now, but it's fragile. You can also test whether or not a
particular
method *is* implemented:
if ($object-can('method_name_to_test')) {
# this works if $object can have methods called on it. It will find
# inherited methods. It can also find AUTOLOADed methods if they've
# already been called and installed in the symbol table
}
A slightly more robust version of that syntax:
if (UNIVERSAL::can($object, $method_name) {
# almost the same thing, but doesn't die a horrible death if, for example,
# $object is undef
}
If you explain the problem you're trying to solve, we might be able to come up with
a better
solution.
Cheers,
Ovid
=
Silence is Evil
http://users.easystreet.com/ovid/philosophy/indexdecency.htm
Ovid http://www.perlmonks.org/index.pl?node_id=17000
Web Programming with Perl http://users.easystreet.com/ovid/cgi_course/
__
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com
BLASTN 2.2.5 [Nov-16-2002]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs, Nucleic Acids Res. 25:3389-3402.
Query= mt0001-av25gc10k167_AV25_01
(110 letters)
Database: gbgene
2,966,325 sequences; 8,818,290,589 total letters
Searching
SOLVED: how do i list the methods connected to a object?
problem solved:
given an arbitrary object, i can now get a dump of all the functions connected to the
object.
print dump_functions( $obj );
sub dump_functions
{
use Data::Dumper;
use Class::Inspector;
my ( $obj ) = @_;
my ( $ref, $methods, @methods );
$ref = ref $obj;
$methods = Class::Inspector-methods( $ref, 'full', 'public' );
@{ $methods } = grep /$ref/, @{ $methods };
return Dumper( $methods );
}
On Tue, Aug 05, 2003 at 12:19:57PM +0200, Martin A. Hansen wrote:
hi
i wonder how i can list all the methods availible from a given object?
martin
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how do i list the methods connected to a object?
hi i wonder how i can list all the methods availible from a given object? martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: SOLVED: how do i list the methods connected to a object?
On Thu, Aug 07, 2003 at 09:01:57AM -0500, Dan Muey wrote:
Cool! 1 quick question why do you have @methods?
sorry old remnant. just delete.
martin
If it's because you use @{ $methods } then $methods would have to be the string
'methods' to be a reference to @methods, which doesn't have any data as far as I can
tell.
Maybe I'm missing something?
Dan
problem solved:
given an arbitrary object, i can now get a dump of all the
functions connected to the object.
print dump_functions( $obj );
sub dump_functions
{
use Data::Dumper;
use Class::Inspector;
my ( $obj ) = @_;
my ( $ref, $methods, @methods );
$ref = ref $obj;
$methods = Class::Inspector-methods( $ref, 'full', 'public' );
@{ $methods } = grep /$ref/, @{ $methods };
return Dumper( $methods );
}
On Tue, Aug 05, 2003 at 12:19:57PM +0200, Martin A. Hansen wrote:
hi
i wonder how i can list all the methods availible from a
given object?
martin
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Re: how do i list the methods connected to a object?
On Tue, Aug 05, 2003 at 08:18:24PM +0100, Rob Dixon wrote: Ovid [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] --- Peter Scott [EMAIL PROTECTED] wrote: The problem here is that it will not print inherited or AUTOLOADed methods. [snip] So traverse the inheritance hierarchy and do the same thing with each class: http://search.cpan.org/author/SBURKE/Class-ISA-0.32/ISA.pm That's certainly a decent 95% solution and if you *really* need it, it's a good idea. The original problem, though, is not one that I want to encourage most people to solve because for most programmers, when things get that complicated, it turns out that there's an underlying design flaw that needs to be addressed. Of course, people seem to get mad when I say that :) I'll second that. Absolutely. If you've created an object and are asking, 'Now what can I do with this object?' then you're not designing software, you're laying bricks. Find a module that, from the documentation, looks like it will do what you want. Then commit to using that module with the documented interface alone. After that, if you find you've made the wrong decision, be prepared to backtrack as far as necessary to redeem yourself. first of all. objects and modules are for software reuse as i understand it. so installing and using modules from CPAN leaves me as a bricklayer! so i have found a module which is fulfilling my needs, but i find it very annoying that i cannot simple dump all the functions connected to a certain object. now im advised to read the module documentation (which can be poor) of this object, AND the module documentation of ALL inherited objects! i find it rediculous to go the documentation path, where you clearly should be able to understand the code based on the code itself! i am aware that OO perl is about abstraction of the code, but this is no good. but enough nagging. even if this is a tricky problem, cant it be solved? if using the ISA.pm as suggested, you are able to track the inheritance solving 95% of the problem, then what is the remaining 5% ? i guess i wish for a widget to go print DumpFunctions( $obj ); does it exist? martin Software built on what a module /can/ do instead of what it's /supposed/ to do isn't a useful thing in any way. Rob -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
how to: perl and gnuplot ???
hi i have script which generates a set of xy coordinates. how can i get the script to generate a gnuplot postscript file from theses xy-pairs? martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
pipe in perl ???
hi how to use an array as input for a external command called within a perl script? im looking to pipe the array to the extarnal program ... martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: pipe in perl ???
On Wed, Jan 15, 2003 at 05:34:59AM -0800, John W. Krahn wrote: Martin A. Hansen wrote: hi Hello, hi again how to use an array as input for a external command called within a perl script? im looking to pipe the array to the extarnal program ... open PIPE, '| somecommand' or die Cannot open pipe to somecommand: $!; print PIPE @array; close PIPE or die Cannot close pipe to somecommand: $!; i figured that much, but that is not the way to solve my gnuplot problem. i need to translate the following commandline to perl: (echo set term post; echo plot '-' w l; cat data) | gnuplot data.ps where cat data is replaced by a pipe of some sort ... gnuplot is tricky because the plot '-' part means that the data is supplied followingly gnuplot is wierd, but i hope perl can unwierd it martin John -- use Perl; program fulfillment -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: pipe in perl ???
On Wed, Jan 15, 2003 at 08:27:13AM -0600, [EMAIL PROTECTED] wrote: Sorry if I already missed a post where you said you couldn't (have had the flu), but could you use one of the various modules in CPAN to control gnuplot instead of trying to manipulate it yourself? hi i did look at it, but i found it confusing. anyhows, i need to learn perl and redirecting output is good to know. martin A quick search: http://search.cpan.org/search?query=Gnuplotmode=all http://search.cpan.org/author/CAIDAPERL/Chart-Graph-2.0/Graph/Gnuplot.pm http://search.cpan.org/author/ILYAZ/Term-Gnuplot-0.5704/Gnuplot.pm Just a thought. http://danconia.org -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: pipe in perl ???
On Wed, Jan 15, 2003 at 10:33:45AM -0500, Bob Showalter wrote: Bob Showalter wrote: [EMAIL PROTECTED] wrote: i need to translate the following commandline to perl: (echo set term post; echo plot '-' w l; cat data) | gnuplot data.ps open(F, | gnuplot data.ps) or die $!; print F set term post\n, plot '-' w l\n; print $_\n for @commands; Oops, forgot the filehandle. That should be print F $_\n for @commands; perfect! i got the same syntax working just before reading this :))) thanx martin close F or die $!; -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
how to recognize a number with regex?
hi what do a regex look like that only matches numbers of the format (the length of the number doesnt matter its the . thats the problem) 1233.1234 or 1234 martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
how to split a perl program on multiple files?
for the sake of order and logic, i want to split my perl script into two files. what is the smart way to do this? i guess there is many ways this can be done, lemmy hear them all ! :o) martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: help! windows makes ^M in my forms?
hi drieux i had a look on you snippet of code. very neat, i didnt know =cut :))). however, im not happy with the regexing solution, since i cant get it to work: $scalar =~ s/\015\012?|\012/\n/g; what is this ^M anywat? carrige return? reading the perldoc -f chomp doesnt tell me if chomp deals with ^M ? actually im interested in how eval deals with ^M, since i suspect my problems is a misinterpretation by eval with regards to ^M... anyway im not sure if i can chomp incomming stuff from a CGI submit ? any help will be appreciated :0) martin On Mon, May 27, 2002 at 08:17:30AM -0700, drieux wrote: On Monday, May 27, 2002, at 07:31 , Martin A. Hansen wrote: my nice cgi forms works beautiful under konq on linux. but the windows machine generates ^M at the and of lines? this makes eval go fubar? how can i prevent this??? http://www.wetware.com/drieux/pbl/RegEx/eolOut.txt may help you get the differences in chomp v. RegExing them to a common standard. Remember that the browsers will do as they will do - and you have to work around that reality ciao drieux --- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
help! windows makes ^M in my forms?
my nice cgi forms works beautiful under konq on linux. but the windows machine generates ^M at the and of lines? this makes eval go fubar? how can i prevent this??? martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
printing from records ?
hi
im able to generate records of this kind:
{
'bleh' = {
'ISHpix' = [],
'gelpix' = [],
'base' = [
''
],
'norm' = [
''
],
'drug' = [
''
],
'organism' = [
''
],
'name' = [
''
],
'cell' = [
''
],
'date' = [
''
],
'tissue' = [
''
],
'quant' = [
''
],
'ISH' = [
''
],
'bg' = [
''
],
'gel' = [
''
],
'primer' = [
''
],
'mt' = [
'bleh'
],
'band' = [
''
]
}
}
now, this is very well.
how do i print a specific record?
i would like to be able to check if a record already exist so i dont overwrite it.
:o)
martin
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Re: printing from records ?
hi felix
the exists check works nicely :)
but i cant get the print to work, using my version of your sub:
sub print_record
{
my ( $record_key ) = @_;
my $record;
my $records;
# read in records
$records = read_recordfile;
foreach $record ( keys %{ $records-{ $record_key } } ) {
print debug . join('', @{ $records-{ $record_key }{ $record } } );
}
return $record
}
$record_key is passed to the subroutine ok (i did check). and the records are read (i
did check using Data::Dumper)
print_record($records, 'bleh');
sub print_record {
my $source = shift;
my $key = shift;
return unless exists $source-{$key};
print Contents of record with primary key $key:\n;
foreach my $field (sort keys %{$source-{$key}}) {
print \t$field: ;
print [ .
join(, , @{$source-{$key}{$field}}) .
]\n ;
}
print \n;
return;
}
But I have a question: what is the functional difference between
[] and [''] in your columns?
good question. i have a hash of hashes of arrays. i want to be able, later on, to push
more values on each secondary hash key - hence the array [''].
martin
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Re: printing from records ?
hi again
im practicing handling structures. im very much a newbie at this so theres prolly
something wrong with my code.
If this is what you want, maybe you have an error in your
read_recordfile?
sub read_recordfile
{
my $records;
{
local ($/) = undef;
open SOURCE, $recordfile or die Can't open file: $!;
$records = eval SOURCE;
die $@ if $@;
close SOURCE;
}
return $records;
}
:-)
martin
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printing element from record ?
hi, im having trouble printing out the key of this record hash:
i wan the result to print:
THIS_HERE
im sure its trivial, but i cant figure it :)
martin
{
'THIS_HERE' = {
'ISH' = [
'3'
],
'ISHpix' = [],
'bg' = [
''
],
'gelpix' = [],
'base' = [
'T'
],
'norm' = [
''
],
'gel' = [
'456'
],
'drug' = [
''
],
'primer' = [
'2'
],
'mt' = [
'foo'
],
'organism' = [
'Human'
],
'band' = [
'1'
],
'name' = [
'abc'
],
'date' = [
'123'
],
'cell' = [
''
],
'quant' = [
''
],
'tissue' = [
'Testis'
]
}
}
i read in the hash using this:
{ #block to control scope
local ($/) = undef; #make this change local so as not to screw up anything else
open SOURCE, $hash_file or die Can't open file: $!;
$hash_ref = eval SOURCE;
die $@ if $@;
close SOURCE;
}
so printing should be something ala:
print $hash_ref - { ? };
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Solved: sort regex trouble!
hi
i finally got it to work. it was very simple ... _if_ you remember that its not td
but td align=foo you are trying to match!
martin
On Wed, Apr 24, 2002 at 11:04:42AM -0400, David Gray wrote:
May I suggest:
(my $A = $a) =~ s/^trtd(\d+)\/td/$1/;
(my $B = $b) =~ s/^trtd(\d+)\/td/$1/;
That's not what he's doing. He's doing:
my ($A) = $a =~ m{^trtd(\d+)/td};
my ($B) = $b =~ m{^trtd(\d+)/td};
Yours leaves everything after the /td tacked onto the end
of $A; mine and his only store the number in $A.
Argh, good catch. I usually do that kind of thing like:
my $A = $1 if $a =~ m{^trtd(\d+)/td};
But I didn't that time :)
Let us know if any of this fixes your problem, Martin...
-dave
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web automation - where to read?
hi im trying to write a scipt that crawls a website. however, with only the documentation from the perl cookbook and some no_good manpages from the LWP modules, im stuck! where can i find som documentation (pref. online) ? or even some examples ? regards martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: web automation - where to read?
On Thu, Apr 25, 2002 at 01:57:07PM -, Felix Geerinckx wrote: im trying to write a scipt that crawls a website. however, with only the documentation from the perl cookbook and some no_good manpages from the LWP modules, im stuck! Would you care to explain what is 'no_good' about the LWP manpages? no good for beginners. where can i find som documentation (pref. online) ? Do you know 'The Web Robot Pages' at thanks, ill have a look :) http://www.robotstxt.org/wc/robots.html? Here you will find a lot of info about all kind of webrobots (or crawlers). If you want more documentation, why not type 'web crawling Perl LWP' in the google.com search box, and find out? Last time I tried it listed about 390 hits. yes, but here i was hoping for some recommendated reading ... -- felix -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] -- martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: regex question
hi john
i implementet your solution. mine actually did work, but yours seemed more logical.
it works nicely.
thank you
martin
On Wed, Apr 17, 2002 at 12:58:07PM -0700, John W. Krahn wrote:
[EMAIL PROTECTED] wrote:
hi,
Hello,
im pasting some more of the lines i need to parse. i guess
im just learning regex and just espesially learning how to
ask the correct questions! heh, dont ask regex without
showing enuf of the stuff you want to parse :)
theres is these three basic entries (skakkebaek is spelled awfully. only skak
matches em all :-) :
Hits Cited Author Cited WorkVolume Page Year
__
[_][667] 279 ...Skakkebaek NE ENVIRON HEALTH PERSP 104 741
1996
[_] 1 SKAKKEBAEK NE EARLY DETECTION TEST26
1981
[_] 3 SKAKKEBAEK NE EARLY DETECTION TEST
1981
then there is these freaks:
this one contains NE in the name and NE in GENE so GENE is truncated if care is
not taken.
[_][718] 18 ...Skakkebaek NE GENE CHROMOSOME CANC 20 412
1997
here the journal name starts with 7
[_] 3 SKAKKEBAEK NE 7 WORLD C FERT STER
1971
here the journal name ends with a digit thus entangling it in the following page
number 101.
[_] 1 SKAKKEBAEK NE ENV HLTH PERSPECT S2 101 1
1993
here is my mathing routine - works with all but the last freak!:
[snip code]
This works with the data above:
while ( DATA ) {
chomp;
my @field = split /\s{2,}/;
shift @field if $field[0] =~ /]$/;
(my $citations) = (shift @field) =~ /(\d+)$/;
shift @field if $field[0] =~ /skak.*ne$/i;
my $journal = shift @field;
my $year= pop @field || '';
my $page= pop @field || '';
my $volume = pop @field || '';
print Citation: $citations\nJournal: $journal\nVolume: $volume\nPage:
$page\nYear: $year\n\n;
}
__DATA__
[_][667] 279 ...Skakkebaek NE ENVIRON HEALTH PERSP 104 741
1996
[_] 1 SKAKKEBAEK NE EARLY DETECTION TEST26 1981
[_] 3 SKAKKEBAEK NE EARLY DETECTION TEST1981
[_][718] 18 ...Skakkebaek NE GENE CHROMOSOME CANC 20 412
1997
[_] 3 SKAKKEBAEK NE 7 WORLD C FERT STER 1971
[_] 1 SKAKKEBAEK NE ENV HLTH PERSPECT S2 101 1 1993
John
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strange cgi error?
hi i have a faulty cgi script which hangs my browser (konq). running the cgi script from a shell shows this first line: Something is wrong?Content-type: text/html so, what is wrong? martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
automagic web query ?
hi im trying to write a script that does a search on a remote website. the script needs to fill in a form field with a search word and save all the results. there is three different form fields on the webpage, but im only interested in the first one. the results comes in 10 per page only, and i would like the script to follow the links so i get all results. can this be done with perl? (i think so). can anyone help me out here? thanks best martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Data::Dumper documentation ?
hi i have read the documentation on Data::Dumper from Learning Perl, Perl Cookbook and perldoc. however, im still very confused. im looking for some beginners documentation and examples. can anyone direct me? :o) martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: Data::Dumper documentation ?
heh - that was exactly half of what i was looking for - how to dump stuff! great :) mayby you can help me out with the second part too? : if i have a datastructure (a hash) dumped to a file using Data::Dumper, how can i recreate the datastructure/hash in another program? if i do something like this: open SOURCE, source.file; undef $/; eval SOURCE; die $@ if $@; close IN; then eval will turn the datastructure into a scalar? but i want it as a hash! or how does it work ? :o) martin ps, love the missile address line! -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
external hashtable
hi
i have some files of the format:
{
'key1' = 'value2',
'key2' = 'value3',
'key3' = 'value4',
'key4' = 'value5',
'key5' = 'value6',
}
the values are large huge chunks of text.
how can i import such a file into a perl script as a hash?
and how can i write the hash to a new file (same format as above)?
best :)
martin
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Re: external hashtable
ok, im on a linux box here. and i do have Data::Dumper. so how would the solution with Dumper work? theres not very much documentation on Dumber in the camel... martin I suggest Data::Dumper, which can do exactly this function. -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
interesting question about variables
hi
i have a loop containing the following block of code. however, first time the loop is
run, $text_link is empty, which it shouldn't be. i cant move the declaration of
$text_link above the if statment, because then the $figure_name would be empty.
now i guess im really missing out on something fundamental here, since i cant figure
out how this issue is solved!
any suggestions will be appreciated
:o)
martin
if ( ( $hash - { $paragraph } ) =~ s/###(\w+.*\.jpg)###/($text_link)/ ) {
$figure_name = $1;
$text_link = $cgi - a({-href = javascript: window.open('$pix_dir/$figure_name',
. '',
. 'status=yes,
. resizable=yes,
. scrollbars=no,
. width=530,
. height=380'
. );
void('');
}, Fig $figure_number );
$figure_number++;
}
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regex question
hi i have a long text file. in this text file several strings of the form: ### filename.jpg ### are embedded. how should a regex look that takes following: text before ### filename.jpg ### text after and returns text before text after and the filename.jpg saved in a $ :o) martin -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
easy way to make a hash of filenames?
hi im trying to make a hashtable of filenames, where the key is a forthrunning number and the value is a filename in a dir. so i have a dir with files: /dir/foo.jpg bar.jpg and i want a %hashtable = ( 1 = 'foo', 2 = 'bar' ) how can this be done ? :o) martin -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Solved: easy way to make a hash of filenames?
neat
works straight away :)
thx
martin
On Mon, Mar 11, 2002 at 02:15:59PM +, Jonathan E. Paton wrote:
so I have a dir with files:
/dir/foo.jpg
bar.jpg
and I want a
%hashtable = (
1 = 'foo',
2 = 'bar'
)
how can this be done ?
Try map:
%hashtable = map { $ctr++, $_ } @files;
Or even:
%hashtable = map { $ctr++, $_ } *;
Of course, I've probably got the syntax wrong - since I
don't use map that often. You can, of course, write many
programs in terms of sub/map like:
sub add {
return map {
#do processing
} @_;
}
which can really annoy your coworkers.
Jonathan Paton
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sort order of hash keys
hi i would like to know if theres a smart way to unwind a hashtable so that the key / value pairs comes out in the same order as they are in the table. :o) martin -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: sort order of hash keys
yeah, i new this was tricky.
my hash keys / values have uneven names so i cant use a sort routine directly. thats
why i would like to get the key / values in the same order as they are in the
hashtable file.
whats the name of that hash modules?
:o)
martin
On Tue, Feb 26, 2002 at 10:28:16AM -, John Edwards wrote:
hash keys are stored unsorted. If you have the following hash
%test = ( one = 1,
two = 2,
three = 3);
and print out the hash key/value pairs.
foreach $key (keys %test) {
print $key is $test{$key}\n;
}
you will find they don't come out in the same order as they were stored.
You can perform a sort on the keys to arrange them in order
foreach $key (sort keys %test) {
print $key is $test{$key}\n;
}
or you can reverse the hash, making the values the keys, and sort on the new
keys
%reversed = reverse %test;
foreach $key (keys %reversed) {
print $key is $reversed{$key}\n;
}
In doing this though, you must be aware that you will lose any data that has
identical values. For example
%test = ( one = 1,
two = 2,
three = 3,
alpha = 1,
beta = 2,
gamma = 3);
%reversed = reverse %test;
foreach $key (keys %reversed) {
print $key is $reversed{$key}\n;
}
will print out
1 is one
2 is two
3 is three
There is probably another/better way of doing this using the comparison
operator =, but I don't know it. There is also a module available that
lets you store and retrieve hashes in a fixed order.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]
Sent: 26 February 2002 09:16
To: [EMAIL PROTECTED]
Subject: sort order of hash keys
hi
i would like to know if theres a smart way to unwind a hashtable so that
the key / value pairs comes out in the same order as they are in the table.
:o)
martin
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appending files
hi i have this very interesting task, and i need some inspiration. i have a directory with say 10 fcgi files (text files): now i would like to have a temp.fcgi file which contains all of the date from the .fcgi files (appended). however, i want my program to update the temp.fcgi file if new .fcgi files are added the directory. i was thinking something like testing the combined size of the .fcgi files compared to temp.fcgi and if it differs then wipe temp.fcgi and generate a new one? how can that be done? -martin -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: appending files
interesting, but no. i can download these .fcgi files from a database and they are quite generic (they contains loads of records). all i wanted is to collect all therecords in one big fcgi file for outputting and sorting. but i may download new .fcgi files regularly and i want them included in the big fcgi file as well. however, i dont want to do the include process with each run of the program! :) martin On Mon, Feb 25, 2002 at 07:48:07AM -0800, Wagner-David wrote: Might be better off using a hash with the filename and say last mod time. Then if a new file or the last mod time is different, then rebuild your data. Wags ;) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Monday, February 25, 2002 06:11 To: [EMAIL PROTECTED] Subject: appending files hi i have this very interesting task, and i need some inspiration. i have a directory with say 10 fcgi files (text files): now i would like to have a temp.fcgi file which contains all of the date from the .fcgi files (appended). however, i want my program to update the temp.fcgi file if new .fcgi files are added the directory. i was thinking something like testing the combined size of the .fcgi files compared to temp.fcgi and if it differs then wipe temp.fcgi and generate a new one? how can that be done? -martin -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] -- -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
unwinding hash or what it is?
hi
i have inherited this piece of code and i have been wondering hard about how i can
print the different @records returned from the subroutine? im not even sure whats on
my hand here. is this a hash of arrays or a hash of array references? and how do i
unwind those?
martin, beginning perl.
my @records = parse_pubmed_fcgi( [ qw(UI AU TI TA VI IP PG DA) ] );
## subroutines
sub parse_pubmed_fcgi {
my ( $keys ) = @_;
my ( @records, $record, $record_id, $line, $key );
my %wants = map { $_ = 1 } @{ $keys };
while ( defined ($line = ) ) {
chop $line;
if ( $line =~ /^(UI)\s*-/ ) {
$key = $1;
if ( $record ) {
push @records, $record;
undef $record;
}
}
if ( $line =~ /^([A-Z]+)\s*-\s*(.+)/ ) {
$key = $1;
push @{ $record-{ $key } }, $2 if $wants{ $key };
}
elsif ( $line =~ /^\s+(\S.*)/ ) {
$record-{ $key }-[-1] .= $1 if $wants{ $key };
}
}
push @records, $record if $record;
if ( wantarray ) {
return @records;
} else {
return \@records;
}
}
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Re: unwinding hash or what it is?
On Thu, Feb 14, 2002 at 10:40:20AM -0500, Chas Owens wrote:
On Thu, 2002-02-14 at 10:19, Martin A. Hansen wrote:
hi
i have inherited this piece of code and i have been wondering hard about how i can
print the different @records returned from the subroutine? im not even sure whats on
my hand here. is this a hash of arrays or a hash of array references? and how do i
unwind those?
martin, beginning perl.
my @records = parse_pubmed_fcgi( [ qw(UI AU TI TA VI IP PG DA) ] );
## subroutines
sub parse_pubmed_fcgi {
my ( $keys ) = @_;
my ( @records, $record, $record_id, $line, $key );
my %wants = map { $_ = 1 } @{ $keys };
while ( defined ($line = ) ) {
chop $line;
if ( $line =~ /^(UI)\s*-/ ) {
$key = $1;
if ( $record ) {
push @records, $record;
undef $record;
}
}
if ( $line =~ /^([A-Z]+)\s*-\s*(.+)/ ) {
$key = $1;
push @{ $record-{ $key } }, $2 if $wants{ $key };
}
elsif ( $line =~ /^\s+(\S.*)/ ) {
$record-{ $key }-[-1] .= $1 if $wants{ $key };
}
}
push @records, $record if $record;
if ( wantarray ) {
return @records;
} else {
return \@records;
}
}
Data::Dumper is your friend. If you have a data structure and you don't
know what is in it just say:
print Dumper(\@Records);
and bingo the data structure is printed out to the screen.
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ok, if Data::Dumper is my friend, how can i print all record fields of type AU only?
martin
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CGI table width
hi
how can i control the width of each column or cell in my table?
i dont exactly know what the following width switch does?
print table({-border = 0, -width = '100%'},
Tr[
td({ width = 75 }, ['', $headline, '']),
td( ['', $hr,'']),
td( ['', $subheadline, '']),
td( ['', $embeddedtable, '']),
td( ['', $hr,'']),
]
);
and by the way. where can i find more description on CGI functions
and especially the switches?
regards
-martin
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width of table cells and CGI ???
hi
i am playing with CGI and tables
how do i set the width of a cell?
my $embeddedtable = table({-border = 0},
Tr[
td(['Title', $title]),
td(['First Name', $firstname]),
td(['Last Name', $lastname]),
td(['E-mail', $email]),
td([$submit, $reset]),
]
);
martin
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RE: width of table cells and CGI ???
thats is pure HTML code... i know!
i want to do it the CGI way!
aint there a -width = 150 switch i can set?
martin
On Thu, 31 Jan 2002, Darryl Schnell wrote:
I usually do TD WIDTH='60' or TD WIDTH='60%' please note that both are different
lengths of the screen.
Darryl
-Original Message-
From: Martin A. Hansen [mailto:[EMAIL PROTECTED]]
Sent: Thursday, January 31, 2002 7:47 AM
To: [EMAIL PROTECTED]
Subject: width of table cells and CGI ???
hi
i am playing with CGI and tables
how do i set the width of a cell?
my $embeddedtable = table({-border = 0},
Tr[
td(['Title', $title]),
td(['First Name', $firstname]),
td(['Last Name', $lastname]),
td(['E-mail', $email]),
td([$submit, $reset]),
]
);
martin
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how to get hash values returned from a subroutine?
hi there
im trying to call a subroutine and get it to return some hash table values. however, i
have two problems.
1. it does not work. theres something wrong with my foreach sentence,
but i cant see what it is. however, the commented foreach sentence
do work?
2. the @return_array needs to be split so i get the values on
seperate lines. how can that be done?
i take this is a very general problem and there is probably many
solution strategies. any suggestion on how to solve my current problem
and any ideas as how to improve the return values from hash issue will be greatly
appreciated.
best regards
martin
#!/usr/bin/perl -w
subroutine;
print \n, @return_array, \n;
sub subroutine {
%hash_table = (
'en' = '1',
'to' = '2',
'tre' = '3',
'fire' = '4',
'fem' = '5',
'seks' = '6',
'syv' = '7',
'otte' = '8',
'ni' = '9',
'ti' = '10'
);
$extract = qw (en tre ni);
# foreach $number (qw en tre ni) {
foreach $number ($extract) {
push (@return_array, $hash_table{$number});
}
return @return_array;
}
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how do i utilize an external hashtable?
hi
if i have a file called table.hash looking like this:
{
'HEADLINE' = 'Carcinoma in Situ',
'SUBHEADLINE' =
'
the precursor cell for testicular germ cell cancer in adolescents and young adults
',
'BODYTEXT' =
'
This site provides information on research, diagnosis and management
of early forms of testicular cancer and is directed to physicians,
researchers and patients.
The site has been developed by members of the CIS Testis Cancer
Research Group led by Professor Niels E. Skakkebæk, MD at the
Department of Growth Reproduction in collaboration with the Danish
Cancer Society, Copenhagen, Denmark.
'
}
how do i access the hashtable with a key and return the appropriate
value?
martin
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CGI and tables ?
hi im trying to build a webpage with perl CGI the object way... the only documentation i have looked at is man CGI can anyone recommend some online documentation? anyway: is it possible to render a table with something like: print $newCGI-start_table(-border='1'); print $newCGI-end_table(-border='1'); doesnt seem to work thou, but i must be missing a lot of parameters. and its only mentioned in the man CGI for the function-oriented way. :o) martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
subroutine returning lines of text
hi im wondering how i can make a subroutine that will return all text lines between certain marks such as START and STOP: text file: START text is here and there is a lot of it STOP so i would like to call the subroutine with the arguments START and STOP (because i may need more starts and stops later) and have the subroutine return the lines between START and STOP in a $. i guess it should be pretty simple, however its out of my reach still :P any help will be appreciated :) ! martin -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
silly beginners problem :)
hi
im trying to make a script to read a textfile with the following format:
TITLE
Welcome to Carcinoma in Situ
i want my script to recognice the TITLE tag and save the following line(s) in $TITLE:
heres what i have done:
while () {
chomp;
if (/TITLE\s*([A-Za-z]+)/) {
$TITLE=$1;
}
}
print $TITLE;
upon script textfile.txt outputfile i get this error:
Use of uninitialized value in concatenation (.) or string in line (the one with print
$TITLE in it)
i think my regex is not doing what i want it to do??? why?
:/
martin
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