how to use perl in windows

hi, for writing perl programs,notepad is used.But what should be done to execute the programs? Also,how can i take input from online databases?like,if i have to get a gene sequence from Genbank,what command should i write in program? thanx in advance, aditi Yahoo! India Matrimony: Find y

vi editor

hi, vi is used only in unix and linux.which editor can be used in windows and is better than notepad. thanx, aditi Yahoo! India Matrimony: Find your partner online.

how to retreive data from internet.

hi, i want to get a DNA sequence from internet for manipulations.i was told that it requires ftp .. but i don't have any idea about it. please tell me how to do it regards, aditi Yahoo! India Matrimony: Find your partner online.

DBI

hi, how to download DBI via PPM? regards, aditi Yahoo! India Matrimony: Find your partner online.

about ppm

hi, i have installed perl 5.8 on windows XP.but the ppm is not working,it says ,it doesn't contain any packages or repositories,also it couldn't connect to activestate. can i get ppm separately or i have to install perl again. thanx in advance, aditi Yahoo! India Matrimony: Find your pa

Re: about ppm

ate.com:80(Bad hostname 'ppm.ActiveState.com') it seems there are no repositories . what should i do?? -aditi Tarun Dua <[EMAIL PROTECTED]> wrote: Aditi gupta wrote: > i have installed perl 5.8 on windows XP.but the ppm is not working,it says > ,it doesn't con

Re: about ppm

ork? -aditi Tarun Dua <[EMAIL PROTECTED]> wrote: Aditi gupta wrote: > hi, > > i have to install bioperl modules. > i gave its full address: > > ppm> install http://bioperl.org/DIST/ > > it said: > > Error: No valid repositories > Error: 500 Can

getting data

hi to all, well, a listing of sequence similarity is as follows: # BLASTN 2.2.9 [May-01-2004] # Query: gi|37182815|gb|AY358849.1| Homo sapiens clone DNA180287 ALTE (UNQ6508) mRNA, complete cds # Database: nr # Fields: Query id, Subject id, % identity, alignment length, mismatches, gap opening

splitting

hi to all, i have a file $seq, in following format: gi|37182815|gb|AY358849.1| gi|2353725|gb|AF015490.1|AF015490 100.00 16 0 0 544 559 320 335 4.2 32.21 gi|37182815|gb|AY358849.1| gi|1335960|gb|U55203.1|BTU55203 100.00 16 0 0 544 559 380 395 4.2 32.21 gi|37182815|gb|AY358849.1| gi|133595

getting online information....

hi to all, i had a file which contained following data: # BLASTN 2.2.9 [May-01-2004] # Query: gi|37182815|gb|AY358849.1| Homo sapiens clone DNA180287 ALTE (UNQ6508) mRNA, complete cds # Database: nr # Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. sta

hii

hello everyone, i have a list of gi accession ids: e.g. gi|5104821|dbj|AP61.1| gi|5104188|dbj|AP60.1|gi|5105654|dbj|AP63.1|gi|26793562|emb|AJ525326.1|ATH525326 etc. is it possible to parse through their summaries available at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleo

Re: hii

supply a list of such gi ids' and get info in a list in the same order as that of gi ids. could u plz help me? thanx -aditi "Randy W. Sims" <[EMAIL PROTECTED]> wrote: On 6/13/2004 11:19 AM, aditi gupta wrote: > hello everyone, > > i have a list of gi access

RE: getting online information....

hi zeus, out of 12 fields (query id; subject id; identity %; alignment length; mismatches; gap openings; q. start; q. end; s. start; s. end; e-value; and bit score) i required only 6 (subject id ; identity % ; alignment length; mismatches; q.start; q.end) and two additional fields: gene and

modules

hi to all, do LWP and HTTP::Request modules come alongwithh perl (activeperl 5.8) or one has to separately install them? Yahoo! India Matrimony: Find your partner online.

Re: getting online information....

Note: forwarded message attached. Yahoo! India Matrimony: Find your partner online.--- Begin Message --- hi zeus, well sorry for bothering you againbut i didn't understand the following line inthe code that you send:   my ($link) = =~ m|href="">|;   please explain it thank you, r

getting columns of 2D array

Hello Everybody, We can get rows of a 2D array as $aref = $AoA[$i]; print @$aref; #will print row 'i' as an array How can I print column 'i' as an array using references? Is there any other way which doesn't require two 'for loops' to print the columns? Thanks in advance, Aditi -- To unsubscr

about substring

Hi everybody, Can we use substr function for a string like: $file = atom 12 N VAL A 1 12.435 13.66 34.6 32.1 32 a N can the decimal numbers be extracted using $x= substr($file, offset, length) (the exact field lenghts of each field are known). Thanks in advance.. -- To unsubscribe, e-ma

extracting coordinates

Hi everyone, That code is working... But my specific problem is as follows: i have a file in which data is stored as HELIX 4 4 VAL 74 LEU 84 1 11 CRYST1 33.020 33.750 75.670 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.00 0.00 0.00 0.0 ORIGX2 0.00 1.00 0.00 0.0 OR

Re: extracting coordinates

Record name "ATOM " 7 - 11 Integer serial Atom serial number. these are the 1st two fields. On 5/9/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > > > - Original Message - > From: Aditi Gupta <[EMAIL PROTECTED]> > Date: Monday, Ma

Re: extracting coordinates

hi john, thanks a lot!! the code worked...:-) On 5/9/05, John Doe <[EMAIL PROTECTED]> wrote: > > Am Montag, 9. Mai 2005 18.52 schrieb Aditi Gupta: > > hi, > > the fields can not be splitted using /s because some fields have common > > boundaries, i.e. some fields

Re: extracting coordinates

hi john, thanks a lot!! the code worked...:-) On 5/9/05, John Doe <[EMAIL PROTECTED]> wrote: > > Am Montag, 9. Mai 2005 18.52 schrieb Aditi Gupta: > > hi, > > the fields can not be splitted using /s because some fields have common > > boundaries, i.e. some fields

columnwise analysis

hi everybody, is it possible to search for a pattern in each column of a file. I've only seen pattern matching operations for a row.. please help!! thanks in advance aditi

Re: columnwise analysis

hi Edward, thanks for the help.. but i didn't really understood the code.. please guide me what documentation should i read for columnwise analysis.. thanks again.. aditi On 5/14/05, Edward WIJAYA <[EMAIL PROTECTED]> wrote: > > On Sat, 14 May 2005 14:12:37 +0800, Ad

Re: columnwise analysis

hey Xavier, thanks a lot.. i'm sure that's going to help.. if i have any problem applying the regex then i'll come back to the list:-) thanks again aditi On 5/17/05, Xavier Noria <[EMAIL PROTECTED]> wrote: > > On May 14, 2005, at 19:47, Aditi Gupta wrote: > &g

Re: columnwise analysis

.. thanks On 5/17/05, Aditi Gupta <[EMAIL PROTECTED]> wrote: > > hey Xavier, > thanks a lot.. i'm sure that's going to help.. > if i have any problem applying the regex then i'll come back to the > list:-) > thanks again > aditi > > On 5/17/05,

extracting columns

Hi everybody, to extract data columnwise from a file, the following code was written with the help of perl experts of this list. the script is as follows: #!usr/bin/perl u

Re: extracting columns

Thanks eveybody.. Knowing how to debug programs will always help. And i'm sorry for not formatting the program according to standard conventions.. i'll do that in future. thanks Thomas for the help:-) On 5/18/05, Ankur Gupta <[EMAIL PROTECTED]> wrote: > > From: Adit

object oriented programming in perl

Hi everybody, I've been doing some general perl coding(not too complicated) for past some time but now i want to learn the object oriented way of programming. I've several books including Perl cookbook, Programming Perl and Beginning Perl (by Simon Cozens).. but now i'm confused which one to re

creating html interface for the perl code

Hi everybody, I've to create html inteface for a perl code. I've to get the input from the user and the data entered in the form has to be processed and output(which is a graph) has to be displayed to the user. But i don't know how to do it... I am adviced to go for CGI, and i only know basic h

how to append blocks in same file

Hi Perlers, I have a file as follows: #block1 aaa aaa #block2 bbb bbb #block3 ccc ccc and i want to append(or i should say merge) these blocks and get a file like this: aaabbbccc aaabbbccc how can this be done using perl? please help.. regards Aditi

Re: how to append blocks in same file

I'm sorry if i gave the wrong impression, i was expecting guidelines, not code. regards, aditi On 6/22/05, Larsen, Errin M HMMA/IT <[EMAIL PROTECTED]> wrote: > > Aditi Gupta wrote: > > Hi Perlers, > > > > I have a file as follows: > > > > #block1 &

Re: how to append blocks in same file

t; On Wed, 2005-06-22 at 09:10 -0500, Larsen, Errin M HMMA/IT wrote: > > Aditi Gupta wrote: > > > Hi Perlers, > > > > > > I have a file as follows: > > > > > > #block1 > > > aaa > > > aaa > > > > > > #block2 > &

Re: how to append blocks in same file

($n+$count)) { my $j=0; #{ print OF "$aoa[$i][$j]\n"; $count++; #} } } -- But I want to do it using the complex data structures. Hence, please explain the points which I couldn't understand. Thanks again, with

cgi problem

Hello Perlers, I'm very new to CGI programming. I'm working with following: Browser: Mozilla Firefox Server: Apache 2.0.54 OS: Windows XP I'm going through the following online tutorial for cgi: http://www.cgi101.com/book/ The 1st cgi code that I wrote is as follows: first.cgi ---

Re: cgi problem

rl. www.activestate.com <http://www.activestate.com> > > ----- > Original Message: > From: Aditi Gupta <[EMAIL PROTECTED]> > To: Perl Beginners > Date: Monday, July 4 2005 08:09 > Subject: cgi problem > Hello Perlers, > > I'm very new to CGI programming. I'm wor

Re: cgi problem

ment this line? i've attached the configuration file. please help. Regards, Aditi On 7/5/05, Aditi Gupta <[EMAIL PROTECTED]> wrote: > > > Hi Ganesh, > > Thanks for your time. I tried that but still its giving 'internal server > error'. > There were

cgi

Hi Ganesh, Thanks for your time. I tried that but still its giving 'internal server error'. There were no unix paths in the httpd configuration file, i found windows paths everywhere. But at one place user directory is given as UserDir "My Documents/My Website" shall i comment this line? please

how to make charts using GD

Hello everybody, I have a perl code that generates a sequence of values which i want to plot on y-axis against 1,2,3... on x-axis. I've read that GD::Graph could be used for it. But I've never done modular programming. Also, I don't know how to install modules from CPAN. Are there any other easier

problem with GD

Hello everybody, I've tried installing GD for Activestate Perl on a Windows XP system. I've downloaded the module from CPAN. But the module contains GD.xs file and hence I've to build it myself. I used C compiler but it is giving many errors and most of them are not being able to locate perl.h, ex

Plotting a 2D chart

Hello Everybody, I have a perl code which produces a string of numbers as output. I want to plot this data on an x-y axes plane. I'm using ActiveState Perl 5.8.6 on a Windows XP platform. Since I don't have direct internet connection, I'm unable to use the online package repositories for installin

Heterogenous array

Hello Everybody, A very happy new year to all of you. Well, I'm trying to create a 2D array in which the 1st array is completely numeric and the other array is a combination of numbers and text. If I write it as : @aoa = ([0..5], [1,2,undef, 3,4]); then the program accepts this array of array, b

Re: Heterogenous array

Hello, The error message "argument "1,2,undef,3,4" isn't numeric" was being displayed. But with Data Dumper it is working. Thanks:-) On 1/2/06, Charles K. Clarkson <[EMAIL PROTECTED]> wrote: > > Aditi Gupta <mailto:[EMAIL PROTECTED]> wrote: > >

GD Graph

Hello Everybody, Is there a way to plot each point separately on a 2D plot using GD::Graph instead of passing the two dimensional array? I want to color differently certain data points in the plot but I couln't find a way to do that. Thanks in advance, Best Wishes Aditi