Re: download a protein sequence from the web using LWP module

[Suvajit Sengupta]

Please avoid posting these kind of requests. The forum is here to sort 
out our problems, not to solve your homework !!


Regards,
Suvajit

[EMAIL PROTECTED] wrote:



SET A 
1.  Write a perl script to find the number of spaces in a given sentence using regular expression.

2.  Write a perl script to take name from command line argument and print 
the inputted name in both lower case and upper case. (use functions)
3.  Write a perl script to evaluate sine series.
4.  Write a perl script to download a protein sequence from the web using 
LWP module

SET B
1.  Write a perl script to convert a given gene into mrna using regular expression 
2.  Write a perl script to check whether a given file format is fasta file or not and if it is so print its sequence only. (use file handles)
3.  Write a perl script to arrange the given set of numbers in descending order and print the largest out of it. 
4.  Write a perl script to download a protein sequence from the web using LWP module


SET C
1.  Write a perl script to find the number of vowels in a given sentence using regular expression 
2.  Write a perl script to duplicate a file  print no. of lines in it. 
3.  Write a perl script for finding the factorial of given number.

4.  Write a perl script to download a protein sequence from the web using 
LWP module

SET D 
1.  Write a perl script to find the percentage of  ATGC using regular expression 
2.  Write a perl script to take line from command line arguments and then count  number of vowels in that line

3.  Write a perl script to calculate a Fibonacci series of given number.
4.  Write a perl script to download a protein sequence from the web using 
LWP module

please give me the answers of these questions.
very-2 thanks.

 



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Execute newgrp system command

[Suvajit Sengupta]

Hi,
 I want to login into a new group using 'newgrp' UNIX command.Every 
newgrp command invokes a new shell.
But when I am trying to execute this system command from a perl script 
the script is terminating and returning the prompt of the new shell .
Can anyone suggest on what can be done to change into a new group from 
within perl script?


Regards,
Suvajit


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Re: Execute newgrp system command

[Suvajit Sengupta]

Hi,
Thanks for the suggestion.
There are some tasks which are directly tied to the group-id. Owing to 
the requirement it may happen my perl script need to switch groups to 
achieve a specific task. So my plan is to change to a new group with new 
grp command after exporting the Environment/required variables from the 
current shell.
After the newgrp system command from a perl script could not satisfy my 
need I tried including the command in a separate .cshrc file and then 
just sourcing that file from a perl script. But this job could not again 
be executed from perl script . The perl script returns error telling the 
sourced file could not be found.
Moreover changing the scripts group permission wont do hold good for my 
case.

I am at bay now !!

Regards,
Suvajit

Shawn Corey wrote:


Suvajit Sengupta wrote:


Hi,
 I want to login into a new group using 'newgrp' UNIX command.Every 
newgrp command invokes a new shell.
But when I am trying to execute this system command from a perl 
script the script is terminating and returning the prompt of the new 
shell .
Can anyone suggest on what can be done to change into a new group 
from within perl script?



Short answer: You can't.

Long answer:

The newgrp command will always run a new shell regardless if it 
succeeds or fails. What you can do instead is set the effective group 
id for the script.


1. Change the script's group to the group you want it to work under 
(see `man chgrp`).


2. Change the script's set group id on execution flag (see `chmod`).

The script will now run under the new group.

See `perldoc perlvar` and search for $) and $(.





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Check empty hash

[Suvajit Sengupta]

Hi,
How can I test whether a hash is empty or not ?
For e.g: I have reference to a hash , say $preCommand and I get
 $preCommands  as {} ,
 Its an empty hash, but it exists and is also defined.
I need to check whether the hash is empty or not.
Does anyone has any clue ?

Regards,
Suvajit

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Re: Check empty hash

[Suvajit Sengupta]

Hi,
I have used Data::Dumper to get the hash. I can test myself that the 
hash is empty.

But how can test in by script that the hash is empty?

Regards,
Suvajit

[EMAIL PROTECTED] wrote:


HI,

You can use Data::Dumper And print the hash reference as,

use Data::Dumper
print Dumper ($preCommands);

If the output is VAR1= {};

Then there are no entries in the has tables

HTH

Regards,
Shaman




-Original Message-
From: Suvajit Sengupta [mailto:[EMAIL PROTECTED]
Sent: Wednesday, November 16, 2005 4:33 PM
To: Perl Beginners List
Subject: Check empty hash

Hi,
How can I test whether a hash is empty or not ?
For e.g: I have reference to a hash , say $preCommand and I get
 $preCommands  as {} ,
 Its an empty hash, but it exists and is also defined.
I need to check whether the hash is empty or not.
Does anyone has any clue ?

Regards,
Suvajit

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Re: Check empty hash

[Suvajit Sengupta]

Thanx, Beau ..it worked !!
Regards,
Suvajit

Beau E. Cox wrote:


Hi Suvajit Sengupta -
 
At 2005-11-16, 01:32:31 you wrote:
 


Hi,
How can I test whether a hash is empty or not ?
For e.g: I have reference to a hash , say $preCommand and I get
$preCommands  as {} ,
Its an empty hash, but it exists and is also defined.
I need to check whether the hash is empty or not.
Does anyone has any clue ?

Regards,
Suvajit
   



Try:

unless( keys %$preCommands ) {
...hash is empty...
}

You can use 'keys %hash' ( or if necessary 'scalar keys %hash' ) to
get a count of the number of hash elements just like @array for arrays.

Aloha = Beau;
[EMAIL PROTECTED]
2005-11-16



 



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Re: Rename a file.

[Suvajit Sengupta]

Hi,
needs further details of the script.
Regards,
Suvajit

Pant, Hridyesh wrote:


Hi
while renaming a file I am getting below error on windows environment..

Couldn't rename  to : Permission denied
Couldn't rename  to : Permission denied
Couldn't rename  to : Permission denied

Can any body suggest me...how to remove this error..

Thanks
Hridyesh

 



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Re: white space between roam and act

[Suvajit Sengupta]

Hi,
To ignore the white space in between ROAM and ACT use /x modifier of 
Perl RE to extend your pattern's legibility by permitting  whitespace 
and comments. Hope that will serve your purpose.

Instead of

if ($msg =~ /roam act/i)

Use

if ($msg =~ /roam act/ix)

Regards,
Suvajit



K.Moeng wrote:


Hello again,

I have rephrased my question from yesterday,

I want to be able to ignore the white space in between ROAM and ACT
that is return the query as ROAM ACT without falling to the else statement.

$msg = $ARGV[0];

$msg =~ s/\/' /ig;

$found = 0;

if ($msg =~ /roam act/i)
{
$name = 'ACTivated';
$found = 1;
}

elsif ($msg =~ /roam dact/i)

{
$name = 'DeACTivated';
$found = 1;
}

if ($found == 1)

print .Thank you..\n;
}

else
{
print Sorry. Your request has not been sent for Roaming.\n;
}


 



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Re: how to find missing value.

[Suvajit Sengupta]

Hi,
 If the array A is a list of consecutive N natural numbers,
then missing number,n = Sum of N natural numbers + Sum of the numbers in 
Array A.


Regards,
Suvajit


Jabir Ahmed wrote:

Hello 
I need to know the best way to get a missing element

from an array.

i have an array @a of size containing values 1 to 101 
with one value missing.


eg: @a=qw( 1 2 3 4 5 6 8 9 10  101);

(the array is not sorted and its only to make it
easier to understand)

now i need to find out the missing value i.e 7 .

if i run a loop then it needs to run  n x n number of
times.

kindly suggest.

Thanks

Jabir



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Re: hi

[Suvajit Sengupta]

Hi,
Can you post the whole script. Possibly you have declared 'use strict' 
in your code or it has been set default.
The problem is that the compiler is demanding explicit declaration of 
the variables that you have used.

declaring @shrimp as :
my @shrimp = COO;
and
foreach my $tuna (@shrimp)
{
   squid=substr($tuna,0,4);
   ...and so on
}

will eliminate the error.

Regards,
Suvajit


ZHAO, BING wrote:


Hi,
  I am doing this simple enough script, but somehow it 
generates error:




open COO, 1898.inf or die Cannot open file 1898.inf:$!;
@shrimp=COO;

foreach @shrimp{
$squid=substr($_,0,4);
$shark=$_..pdb;
system \rm dali.lock; #ignore this part
system dalilite ~readbrk pdb1898/$shark $squid; #ignore this part
}


Global symbol @shrimp requires explicit package name at 
./pdbReadbrk2000.pl line 19.

syntax error at ./pdbReadbrk2000.pl line 21, near foreach @shrimp
Global symbol $to requires explicit package name at 
./pdbReadbrk2000.pl line 21.



thank you all, what did I do wrong?

best,



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Re: Problem reading data from an HTML file

[Suvajit Sengupta]

Nath, Alok (STSD) wrote:


Can anyone point out why it is not outputting anything ?

It is suppose to read an HTML file and display the table contents.

One thing I observed is - It is not entering the for loop and I s 
not printing anything ( in print Table found at , join(',',

$ts-coords), :\n;)



#!/usr/bin/perl

use warnings ;
use strict ;
use LWP::Simple ;
use HTML::TableExtract ;

my $html_string = test.htm ;
my $te = new HTML::TableExtract(depth=3,count=4,gridmap=1) ;
$te-parse($html_string);

foreach my $ts ($te-table_states) 
 


Instead of using $te-table_states try using $te-tables in the above line.


{
print Table found at , join(',', $ts-coords), :\n;

	foreach my $row ($ts-rows) 
	{

print join(',', @$row), \n;
print @{$row} ,\n;

}
}

 



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[Fwd: Re: Infinite loop problem]

[Suvajit Sengupta]

Hi Vineet,

 Since Perl provides strong feature of pattern matching of Regular 
Expn you should use that.
Just read in the pattern GAGAGAGAGGA from the file and store it in a 
scalar variable.

You can refer to the following perl code snippet for getting  yout job done.
#! /usr/bin/perl
my $x = 'GAGAGAGAAAGG';
$x =~ s/G/GLY/g;  # Search for pattern G globally and replace it with 'GLY'
$x =~ s/A/ALA/g;  # Search for pattern A gloablly and replace it with 'ALA'
print $x;  # Print replaced string

1. Read in the string from your file .
2. Search and replace the string as required
3. Write the string in another file
The code wont take more than 10-12 lines. And the beauty is you dont have to 
iterate over your string.

Regards,
Suvajit


Vineet Pande wrote:


Dear Perl Guru:

I want to write a script which takes input a text file with sequence 
of alphabets (amino acids) like GAGAGAGAGGA etc. and converts them 
to a three letter corresponding code [G= GLY, A= ALA]. The output 
should be then written to another file. I wrote the following script, 
but it seems it goes in an infinite loop and only prints GLY GLY 
GLYinfinitely for an input of GAAAGAGAAGA etc. Any suggestions? 
Thanks in advance

-Vineet


#!/usr/bin/perl
use warnings;

my $fasta_file = fasta.txt; #this contains single letter code#
chomp $fasta_file;
my $charmm_file = charmm.txt; #this is expected to have three letter 
converted#

unless (open (IN, $fasta_file) )
{
print Cannot open file \fasta_file\\n\n;
exit;
}

open OUT, $charmm_file or die;
@protein = IN;
close IN;
$protein = join( '', @protein);
$protein =~ s/\s//g;

for ( $position=0; $position  length $protein; ++$protein )

{
$aa = substr($protein, $position, 1);


   if ($aa eq 'G') {
   $praa = GLY ;
   print OUT $praa;
   }
elsif ($aa eq 'A') {
   $prab = ALA ;
   print OUT $prab;
   }
else {
exit;
 }
  }

  close OUT;

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