RE: regexp matching- real simple!-GOT IT!
Thanks,
-Nandita
-Original Message-
From: Nandita Mullapudi [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 13, 2003 5:16 PM
To: [EMAIL PROTECTED]
Subject: regexp matching- real simple!
This has to be really easy- but I cant get it to work:
I want my script to carry out a loop only if the number stored in
$diff is positive,
so i say
if ($diff =~m/^[-\d+]/) {blah blah}
but it won't work. why?
TIA
-Nandita
--
Is the number stored as a string? Probably not. Why not use:
if ($diff > 0) {blah blah}
Chris.
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regexp matching- real simple!
This has to be really easy- but I cant get it to work:
I want my script to carry out a loop only if the number stored in
$diff is positive,
so i say
if ($diff =~m/^[-\d+]/) {blah blah}
but it won't work. why?
TIA
-Nandita
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previous element in a list
I have a list of elements- and for every element in the list, I want to carry out an operation with the previous element or the next one, as the case might be, how do I tell perl to look at the previous element? t.i.a -Nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
was re readline() on closed filehandle FILE
i just found the problem- bad formatting of filenames in my list of files.. thanks! -nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
readline() on closed filehandle FILE
Hi all,
am using the following script to parse a long list of files. funnily
enough, it works fine when i try a couple sample files, but when i'm
using a long list of files, it comes up with this error:
readline() on closed filehandle FILE at hashing22.pl line 29, line
13 (#1)
(W closed) The filehandle you're reading from got itself closed
sometime
before now. Check your logic flow.
i dont know what could be causing this- any ideas?
here's the script:
#!/usr/bin/perl-w
# takes a file where the first line specifies query length, puts in ahash
# the seqid and numbers listed, adds up the numbers, divides by qlen
# and give len coverage.
use diagnostics;
$out_dir = "post_parsing_len_cov_files";
mkdir $out_dir, 0777 unless (-e $out_dir);
$| = 1;
$files= "./listofnames2";
open (FH,"$files") or die "cannot create list :$!";
while () {
push (@list, $_);
}
foreach (@list) {
$filename=$_;
open (FILE, $filename);
open (HASH_OUT, ">$out_dir/$filename.stats");
my %hash;
while ()
{
if (/^Query : (.*)\S/m){
$qname = "$1";
print HASH_OUT "Query : $qname\n";
}
else
{
if (/^qlen = (\d+)/m){
$qlen = "$1";
print HASH_OUT "querylen = $qlen\n";
}
else
{@line = split (/\n/);
foreach $line (@line){
($key,$value) = split (/:/);
$hash {$key} = $value;
#print " $value";
@nums = split (" ",$value);
#print "$key: @nums";
$tot = &total(@nums);
$cov = $tot/$qlen * 100 ;
if ($cov >= 50){
print HASH_OUT "$key : $cov\n";
}}}
}}}
close FILE;
sub total {
my $sum;
foreach (@_){
$sum += $_;
}
$sum;
}
--
a typical file to be read by this script is would look like this:
Query : MAL13P1.227_ubiquitin-conjugatin
qlen = 278
>CpType1H_3652:111 81
>CpIowa_1214.266:111 121
>CpGSS_AQ842837:98
>CpType1H_3631:118
>CpIowa_1214.272:118 74 26
>CpIowa_1214.275:77 90 141 17 10 17
>CpEST_AA390251:117
>CpEST_AA390240:102
>CpType1H_3267:77 143
>CpGSS_AQ842682:98
------
SOME files also don't have any lines in them after the first two.
any suggestions on improving my long winded coding skills (or lack
thereof) are most welcome.
thanks,
-nandita
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picking numbers out of a file and operating on them (fwd)
How does one tell perl to perform mathematical operations? I have a file with a series of items like this: >BLAH1 Length = 500 Identities = 20/100. >BLAH2 Length = 400 Identities = 30/70 For each item called BLAH, I want to pick the denominator in Identites and divide by Length and calculate percentage. Eg. for BLAH1: 100/500 * 100 = 20% and later , print all BLAHs for which the value is >50%. I csn write reg exps to find the numbers i am interested in, but am not sure how to go further.. thanks, -nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
picking numbers out of a file and operating on them
How does one tell perl to perform mathematical operations? I have a file with a series of items like this: >BLAH1 Length = 500 Identities = 20/100. >BLAH2 Length = 400 Identities = 30/70 For each item called BLAH, I want to pick the denominator in Identites and divide by Length and calculate percentage. Eg. for BLAH1: 100/500 * 100 = 20% and later , print all BLAHs for which the value is >50%. I csn write reg exps to find the numbers i am interested in, but am not sure how to go further.. thanks, -nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
HTML::SimpleLinkExtor
Hallo All,
I tried to solve my problem using HTML::SimpleLinkExtor and
HTML::LinkExtor.In both cases I got a similar error message.
my scrpit is as follows:
#!/usr/bin/perl -w
use strict;
use HTML::TreeBuilder; #Parser that builds HTML
syntax
tree
use HTTP::Request::Form; #Construct HTTP::Request
objects for
Form
processing
use HTML::Parse;
use HTTP::Request::Common;#Construct common HTTP::Request
objects
use LWP::UserAgent; #Provides an object for
clients,
UserAgent object acts as a
browser
use LWP::Simple;
use URI::URL;
use HTML::SimpleLinkExtor; #Module to extract Links
use Data::Dumper;
use HTTP::Headers;
# Upload the Website
my $url = url 'http://some_host/navitune.html';
my $ua = new LWP::UserAgent;# Create a
LWP::UserAgent
object
$ua->requests_redirectable ( ['POST'] );# Add METHOD POST for
redirection
my $res = $ua->request(POST $url);
# Parse the website and extract the Form
my $tree = new HTML::TreeBuilder->parse( $res->content);
$tree->eof(); #Signals
that
you are finished with parsing content into
the tree
my @forms = @{ $tree->extract_links('FORM') };
# The first Form
my $f = HTTP::Request::Form->new( $forms[0][1], $url ); #Constructs a
new
form processor
#$f->dump(); # Prints the extrachted Form on the STDOUT
# Fill and Send the Form
$f->field( 'wav_file', 'st11.wav' );# retrieves or sets a
field-value ,
where the fieldname =wav_file
,fieldvalue
= st11.wav, which is also the file to be
Uploaded
my $response = HTTP::Response->new;
$response = $ua->request($f->press('submit')); # Practically it clicks
the
Submit button and the form is
sent.
# Response from the Serverside
$response->as_string(); #as_string is a method of
HTTP::Request.It
returns the text version of the request
object
as a string with \n placed after each
line.
# Parse the website and extrach the first three Links using
HTML::LinkExtor
my $linkparser = HTML::SimpleLinkExtor->new(); #Create
SimpleLinkExtor
object
$linkparser->parse($response);#Parse
response
my @all_links = $linkparser->links;#Gets a list
if links
print Dumper \@all_links; #Print list of links out
when i execute this script, I get this: $VAR1 = [ ];
I donot have much experience in perl programming, so i cannot figure out the
mistake or am I doing some mistake in my scrpit ?
I would be thankful if somebody could invest time to answer my question.
thanks in advance
nandita
Nandita Shenvi
Appartment Nr. 707
Westhoffstr. 15
44791 Bochum
Germany
0234/5844456
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LWP::UserAgent
Hi all,
I have a perl script that fills submits a HTML form with METHOD POST and
input type file.
#!/usr/bin/perl -w
use strict;
use HTML::TreeBuilder;
use HTTP::Request::Form;
use LWP::UserAgent;
use URI::URL;
# Upload the Website
my $url = url 'http://some host/navitune.html';
my $ua = new LWP::UserAgent;
my $res = $ua->simple_request(POST $url);
# Parse the website and extrach the Form
my $tb = new HTML::TreeBuilder->parse( $res->content);
my @forms = @{ $tb->extract_links('FORM') };
# The first Form
my $f = HTTP::Request::Form->new( $forms[0][1], $url );
$f->dump(); # Prints the extrachted Form on the STDOUT
# Fill and Send the Form
$f->field( 'wav_file', 'st11.wav' );# wav_file is the name of the
input
field and st11.wav is the file
to be
Uploaded
my $response = $ua->request($f->press('submit'));
# Response from the Serverside
print $response->as_string;
The webserver should send me a list of macthes but i get a response saying :
302 Found
Found
The document has moved http://somemhost/cgi-bin/navitune_web?2+input2.wav";>here.
I think there is some problem with redirect, because when I go to:
http://somemhost/cgi-bin/navitune_web?2+input2.wav
i have the list there, but I would like to store th elist straight away in a
file.
I have tried using methods from LWP::UserAgent like simple_request and
redirect_ok but it did not work.
I would be gratefull for anyhelp, thanks for ur time
nandita
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html::form problems
Hallo All,
I have checked the mailing list and some where in 1999 a person had a
similar problem and i could not find any appropriate answer to the questions
that he had.
anyway, i will try to explain:
I want to write a Perl program to upload a file to a web server. Please
note that I'm NOT looking for a script to create a html form with in it,
and I'm NOT looking for a cgi-script to handle the server side of the
upload.There exist a upload.c program on the webserver. What I'm looking for
is a standalone program that connects to a web server and uploads a file.
I tried to solve the problem using LWP::UserAgent.
my scrpit is as follows:
#!/usr/bin/perl -w
use LWP::UserAgent;
use HTML::Form;
use HTTP::Request;
use URI::URL;
$url = new URI::URL("http://some host");
$ua = new LWP::UserAgent;
$req = new HTTP::Request(POST, 'http://some host/navitune.html');
;
$resp = $ua->request($req)->as_string();
print "$resp\n";
this print out the whole html , i would like to fill the form in the HTML
and send it to the webserver.
I am pretty new in perl and would be grateful for ur help.
thanks
nandita
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problems with variables
hallo All, My problem, i will explain in terms of an example: I have variable $e-mail the value of the var is an e-mail address, now I would like to to store the value of the variable under another name for example email_id001 or email_id$i, where $i is just a interger. The problem may seem simple to many of u, but i do not have much experience in perl and would be rather grateful for ur help. thanks nandita Nandita Shenvi Appartment Nr. 707 Westhoffstr. 15 44791 Bochum Germany 0234/5844456 _ STOP MORE SPAM with the new MSN 8 and get 2 months FREE* http://join.msn.com/?page=features/junkmail -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Problem with Mail::MboxParser
Hallo All,
I am new in perl and will be grarefull for any help.
my perl script is as follows:
#!/usr/bin/perl -w
use lib "/home/shenvi/share/man/man3";
use IO;
use Mail::Internet;
use MIME::Tool;
use Mail::MboxParser::Mail;
use Mail::MboxParser;
#USE OF Mail::MboxParser
my $mb = Mail::MboxParser->new("(\*STDIN)", decode => 'HEADER');
for my $msg ($mb->get_message) {
print $msg->header->{FROM}, "\n";
$msg->store_all_attachment('/home/shenvi/perl/tmp');
}
when i try to run this scrpit I keep on getting this error:
Error: The filename you passed to open() does not refer to an existing file
at Teststrip.PL line 31
in the above case line 31 is
my $mb = Mail::MboxParser->new("(\*STDIN)", decode => 'HEADER');
thanks
nandita
Nandita Shenvi
Appartment Nr. 707
Westhoffstr. 15
44791 Bochum
Germany
0234/5844456
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parsing out contents
I have a parsed output in a single file, that looks like this Pf_sumthing.bln blah blah Pf_sumthingelse.bln blah blah and so on, I want to parse this file such that i create 80 or as many little files, each has the filename as its respective Pf_something and content has the blah blah. can anybody point me in the right way? this is what i've been trying to do -use split (/Pf.*\w/) and try to separate the contents..but i'm not getting there.. t.i.a. nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
RE: printing output to a file
Thanks ALL for the quick help! i realised my mistake, "open" shd be outside the loop.. :) :) (scripts that work, very pleasing!) nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
printing output to a file
hello list
i am trying to print the output of a parsing script to a file- the way it
is right now, the print commands are within a foreach loop, and it prints
to the screen. in order to get the entire output into a file, i'm using a
simple set of commands like so:
foreach my $key (keys %alignments) {
print "$key\n\n", $alignments{$key}, "\nXXX\n";
open (OUT, '>outputfile.txt') or die "couldn't";
print OUT "$key\n\n", $alignments{$key}, "\nXXX\n"
}
print $ending_annotation;
exit;
the output to the screen prints the entire output correctly, but when i
open the file output.txt i get only the last item in my output, not the
entire list..
any help appreciated..
many thanks
nandita.
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Re: inserting a single word in every file
Hi Thanks alot for your help, i finally got my word inserted just once in every file (was re ALIGNMENTS..) yea...am kinda slooow! :) nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
Re: inserting a single word in every file
Thanks, but I forgot to mention in the beginning that i need to make this
modification only ONCE in my file- the ">" character comes up every few
lines, but I only want the title "ALIGNMENTS" in the beginning..i.e, it
shd not replace all the ">"s in my file..
?
sorry about that!
-thanks,
nandita
On Wed, 21 Aug 2002, Sudarshan Raghavan wrote:
> On Tue, 20 Aug 2002, Nandita wrote:
>
> > Thanks for your message, this is how it looks:
> >
> > beginning of file :
> >
> > Reading High Probability Sequences producing High-scoring Segment Pairs:
> > Frame Score P(N)N
> >
> > EMBL:B88446 CpG0200B CpIOWAgDNA1 Cryptosporidium parv... +375 0.391
> > EMBL:AQ935741 CpG2625B CpIOWAgDNA1 Cryptosporidium pa... +174 0.631
> > EMBL:AQ855708 CpG1711B CpIOWAgDNA1 Cryptosporidium pa... -171 0.891
> > EMBL:AQ935455 CpG2480A CpIOWAgDNA1 Cryptosporidium pa... +269 0.971
> > EMBL:AQ450103 58A04.x1 CpIOWAM13mp18gDNA1 Cryptos... -169 0.981
> > EMBL:AQ254466 CpG0842A CpIOWAgDNA1 Cryptosporidium pa... +268 0.991
> > EMBL:AQ935528 CpG2517B CpIOWAgDNA1 Cryptosporidium pa... -267 0.9981
> > EMBL:AQ854869 CpG2093B CpIOWAgDNA1 Cryptosporidium pa... +267 0.9981
> > EMBL:AQ450236 59E03.x1 CpIOWAM13mp18gDNA1 Cryptos... -165 0.1
> > EMBL:AQ003639 CpG0296A CpIOWAgDNA1 Cryptosporidium pa... +25 0.01
> >
> > "ALIGNMENTS:"
> >
> > >EMBL:B88446 CpG0200B CpIOWAgDNA1 Cryptosporidium parvum genomic, genomic
> > survey sequence.
> > Length = 508
>EMBL AQ935528 Cp
above is the word "ALIGNMENTS:" which is not present and which i'd like
to
> > add in each file. i figure i'd have to write out a reg exp- something like
> > "newline followed by ">" ...but am not able to get a good start..-and dont
> > know how to go abt the actual task- figured it had to do with "printing
> > to" a variable in which i stored the file value...
> > am chewing on it..
>
> You don't have to check for the newline just a if (/^>/) would do
> This assumes that the files to be modified are given in the command line
> If you are getting it some place else, empty @ARGV and add these files to
> @ARGV.
>
> #!/usr/local/bin/perl -w
> use strict;
>
> $^I = '~'; # perldoc perlvar, inplace edit and creates a backup filename~
> while (<>) {
> print "ALIGNMENT:\n" if (/^>/);
> print;
> }
>
> The same can also be done as an oneliner
> perl -i~ -pe 'print "ALIGNMENTS:\n" if (/^>/);' *.txt
>
> Note: This will create a backup of all the files it processes, for e.g.
> if the file names1.txt the original file will be backed up as names1.txt~,
> the same as above.
>
> perldoc perlrun and read through the sections that explains these flags.
> You can replace the *.txt with the list of files that you want modified.
>
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inserting a single word in every file
Hello all, I have a list of files, and need to insert a word somewhere in the middle- the files begin with a list of sequence names followed by alignments for each sequence, and i'd like to insert the header "ALIGNMENTS" before they begin.. Any starting ideas / pointers for me? many thanks and have a nice day... -nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
use of uninitialised value..
thanks, all, the script is working!! small pleasures of life.. cheers! -nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
use of uninitialised value...
i'm trying to run a perl script written to parse a file, and it runs fine the way it is written, however, after making little changes to accomodate my file, i get inundated with the following message "Use of uninitialized value in hash element at modif2.pl line 90" can any1 tell me what this means? many thanks nandita -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
