puzzled

Hi there, I am puzzled by the 'build_seq' subroutine in following code. #!/usr/sbin/perl -w use strict; use vars qw($USAGE); # random sequence generator # # -c=1 option will cause prot sequences to be built # using vertebrate aa frequencies, # with option -a putting a 1st methionine residues on.

Exponential numbers

Dear all, I have a table that has exponential numbers of the type 0.203E-2 and I will like to reformat getting rid off the exponential so that the previous number would look when printed as 0.00203. Is there any easy way to do this? Any help welcome. Regards, Pedro -- To unsubscribe, e-mail:

mathing only one type of characters

this problem will be greatly appreciated. cheers *** PEDRO A. RECHE , pHDTL: 617 632 3824 Bioinformatics Research Scientist FX: 617 632 4569 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Molecular Immunology

processing text in perl script

in advance for any positive response. cheers *** PEDRO A. RECHE , pHDTL: 617 632 3824 Bioinformatics Research Scientist FX: 617 632 4569 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Molecular Immunology

Problem with Getopt::Std

($A); } else { usage; exit; } if ($opt_b) { $B = $opt_b; chomp($B); } else { usage; exit; } } -- *** PEDRO A. RECHE , pHDTL: 617 632 3824 Bioinformatics

Re: help parsing file

John W. Krahn wrote: Pedro Antonio Reche wrote: Hi, I am interested in parsing the file at the bottom of this e-mail in order to extract the string between following /product=, /protein_id=, /db_xref= and /translation=, and that for each of the segment separated by the string CDS

Re: help parsing file

Bob Showalter wrote: -Original Message- From: Pedro Antonio Reche [mailto:[EMAIL PROTECTED]] Sent: Tuesday, December 17, 2002 7:22 PM To: [EMAIL PROTECTED] Subject: help parsing file ... I am not please with it, as it generates an empty element in the hash from

help parsing file

61 ttaataatat ataaga gtacattaat attata aaataa tttagtgtct // *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44

parsing two column file

. Any help welcome. Cheers -- *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A, EM: [EMAIL

Re: parsing two column file

{ print $hash{$array2[$i]} from $array2[$i-$j] to $array2[$i]\n; $j=0; } } *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical

file with unique records

{ $SEQ{$1}.= $line; } } close TMP } However, I find that *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED

matching extracharacters

help in doing this will be very appreciated. Cheers Pedro *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street

problems with libwww-perl module

object, not a HTTP::Response object at ./ranseq.pl line 19 As I said I am a little bit lost, and I will be very happy for any help on the subject. Cheers *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer

problem with NET::FTP script

]/; my $pdbentry = $key; my $rcsbfile = pdb . $key . .ent.Z; $ftp-get($ftpdir/$rcsbfile, $dir/${pdbentry}.pdb.Z)or print Can't get $pdbentry\n; system(gunzip $dir/${pdbentry}.pdb.Z); } } -- *** PEDRO A. RECHE

help parsing file

] MIHDSLTTRSTLRTLNDAAPRVINDILYQHPKWISNYQLIEFNSTTHTLIVDSESGQDLVTGIFNLYDQNRNHAGYSCLG *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A, EM: [EMAIL PROTECTED

Re: help parsing file

Hi Drieux, thanks a lot for the help. Your program is working very well. My best wishes for you. Pedro *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School

weird characters

-- *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A, EM: [EMAIL PROTECTED] Boston, MA 02115URL: http

string question

]; } *** PEDRO A. RECHE , pHDTL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A, EM: [EMAIL PROTECTED] Boston, MA 02115URL: http://www.reche.org ***

Telling the cgi to wait

-- *** PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School,EM: [EMAIL PROTECTED] 44 Binney Street, D1510A, EM: [EMAIL PROTECTED] Boston, MA 02115 URL

digits in string

Hi all, how can check if one string only contains digits? Cheers *** PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute,FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED

help with form

; *** PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute,FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A,EM: [EMAIL PROTECTED] Boston, MA 02115 URL: http

help with form

; *** PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute,FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A,EM: [EMAIL PROTECTED] Boston, MA 02115 URL: http://www.reche.org ***

uploading file

at the same time. I am using the form tag multipart/form-data and input type=file, but as I said I do not how to tell to program to use one input or the other. If someone could send me an example script dealing with this issue it will be great. Regards, Pedro Reche

deleting white spaces

welcomed. Cheers *** PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute,FX: 617 632 4569 Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D1510A,EM: [EMAIL PROTECTED

printing lines chunk

Hi All, I have a long line with no blank characters and I would like to insert a return character every 60 characters. Any idea welcome. Regards Pedro *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist

DELETE BLANK LINE

-- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Harvard Medical School, EM: [EMAIL PROTECTED] 44 Binney Street, D610C

ONE MORE TIME

NEPSKAAALL AFDYFCTMRF EPHVCDFWND NIIHEIEAIN GTYCKGQPWC MSMILLGDCI YGMTLHEGVE PNDVLWHCSS FRKHECMQVP PHWQRPQCSY KCNKIPGNRR TFQKTKNMHV LWAESRNSMG *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist

submit hitter

split to @_ is deprecated at ransep.pl line 23. Any clue about what is going on here? Cheers -- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber

split a file

MALPVTALLLPLALLLHAAR---PSQFRVSPLDRTWNLGETVELKCQVLL Sequence tree: == ((gi|38145|emb|CAA4278:0.003018, gi|7438693|pir||S256:0.003018):0.002338, gi|1168854|sp|P41688:0.005357); *** PEDRO a. RECHE gallardo, pHD

split a file

MALPVTALLLPLALLLHAAR---PSQFRVSPLDRTWNLGETVELKCQVLL Sequence tree: == ((gi|38145|emb|CAA4278:0.003018, gi|7438693|pir||S256:0.003018):0.002338, gi|1168854|sp|P41688:0.005357); *** PEDRO a. RECHE gallardo, pHD

emptying an scalar variable

Hi all, can anyone tell me how to empty an scalar variable once a condition is met? I am doing something like this: $line .= $_ if ($_ =~ /something/) { print $line; empy $line; } Any help welcome? -- *** PEDRO

HELP FORMATING A FILE

; -- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Harvard Medical School, URL: http://www.reche.org 44 Binney Street, D610C, Boston, MA 02115 ***

HELP WITH A FORM

give an example of how this thing could be done it will be of great help. Best regards, Pedro *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber

HELP WITH AWK2PERL SCRIPT

] =~ /\./)) { print $_; } } I will be very happy if anyone could help me to understand the script. I am particularly lost with the eval function. Cheers -- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist

output filenames as inputs

the program as it follows: program.pl input1 input2 filename.out program.pl should use take input1 and input2, do the job, and write the data to a new file named filename.out. Any help wellcome. Cheers -- *** PEDRO a. RECHE

PARSING A FILE

-- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Harvard Medical School, URL: http://www.reche.org 44 Binney Street, D610C, Boston, MA 02115 ***

ONE LINE PERL COMMAND

. -- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED] Harvard Medical School, URL: http://www.reche.org

SPLIT QUESTION

Hi all, How can I split a string of caracters -any but blank spaces- into the individual caracters? Cheers - -- *** PEDRO a. RECHE gallardo, pHDTL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX

Re: PARSE CLUSTAL

})" should have been taking care of this but, at least in my machine, it is not. The attached file contain an input file, so you can check what I am saying. Any help will be welcomed, Pedro Reche -- ******* PEDRO a. RECHE gallardo, pHD T

PARSE CLUSTAL

-SETDAGYFDDFTSEADMAKYADVFKRQDKLTAMVDDSAVSSKL I have tried to solve the problem but I have not found an elegant solution, and any suggestion will be welcomed Cheers Pedro Reche -- *** PEDRO a. RECHE gallardo, pHD

Re: PARSE CLUSTAL

"parseclustal.aln" (see attachement), but instead the result is that seen in the attached badparseclustal.aln. I run the program with the following command "parseclustal.pl clustal.aln > output" Please, let me know if you find a solution and thanks for your help