beginning perl for bioinformatics tisdall

... Decree Enforcement (OCDE) will be scanning all computer files for compliance starting tomorrow, and for each document that’s found to be in violation, the responsible parties will be forced to forfeit ... train her in the ways of Perl V and prepare the Engine of the Parrot for Perlitus Sixtus. It works! This file has been properly identified as one that needs to be reformatted tofit on the paper, ... started for eachscript, making Perl’s automatically updated $$ variable the most appropriate backup-file extension for use within in-place editing scripts 4.8 C ONVERTING TO LOWERCASE OR UPPERCASE Perl

Ngày tải lên: 06/08/2014, 03:20

... easier with Perl For example, Perl s test for a... operators, and operator precedence • man perlop man Lingua::EN::Inflect # conditional pluralization, and more42 • # Perl' s Plain ... Old Documentation system • man perlpod # Perl' s documentation-retrieval utility • man perldoc # AWK to Perl source-code converter • man a2p • http://perldoc .perl. org/index-functions.html ... sooner... make it easy for programmers using other Unix tools to migrate to Perl, which is why Perl comes with a sed-toperl translator Guess what Perl comes with an awk-to -perl translator

Ngày tải lên: 06/08/2014, 03:20

... automatically load fields into @F, as discussed in part 1.For this reason, split is primarily used in Minimal Perl for secondary splitting Forinstance, input lines could first be split into fields ... LISTS 223Table 7.8 lists some of Perl’s most useful functions for list processing—which providereordering, joining, filtering, and transforming services, respectively, for lists Thetable also shows ... opposite direction with Perl functions, as illustrated in table 7.9 You’ll learn how Perl’s sort and grep functions work soon, but for now, all youneed to know is that the Perl examples in the table

Ngày tải lên: 06/08/2014, 03:20

... eliminates the most common need for it rea-7 To learn about the first Perl beautifier, see http://TeachMePerl.com/perl_beautifier.html. Table 8.5 String operators for concatenation and repetition ... FOR EACH LINE OF INPUT ##### 16 ( $title, $artist, $rating )=@F; # load fields into variables 17 $fcount=@F; # get field-count for line 18 if ( $fcount != $num_fields ) { # line improperly formatted ... treatment For help in spotting these syntax errors and others, try running your code through a beautifier You can learn about and download the standard Perl beautifier fromhttp://perltidy.sourceforge.net.7

Ngày tải lên: 06/08/2014, 03:20

... $index=rand @fortunes; # select random index Listing 9.4 The fcookie2 script Trang 1028 delete $fortunes[ $index ]; # mark fortune undefined29 @fortunes=grep { defined } @fortunes; # remove ... next throw caution to the wind, for-sake all control over indexing, and see what fortune has in store for those who ran-domly access arrays. 9.1.4 Telling fortunes: The fcookie script In the ... form of a command called fortune, which displayed ahumorous message like you might find in a verbose fortune cookie We’ll pay homage to that comedic technological breakthrough by seeing how Perlscripts

Ngày tải lên: 06/08/2014, 03:20

... commands; done # Form 1 Table 10.10 The select loop for Perl use Shell::POSIX::Select; select () { } # Form 0 select () { CODE; } # Form 1 select (LIST) { CODE; } # Form 2 select $var ... & description have this format in $perlpage: 8 # perlsyn Perl syntax 9 10 # Loop creates hash that maps man-page descriptions to names 11 while ( $perlpage =~ /^\s+(perl\w+)\s+(.+)$/mg ) { ... description of its subject, in this format: perlsyn Perl syntax As illustrated in the figure, the role of perlman is to let the user select a man-pagename for viewing from its short description

Ngày tải lên: 06/08/2014, 03:20

... the submitted form 20 $form.=startform(-method=>'GET', -action=>''); 41 $form.=checkbox_group(-name=>'flavor', 42 -Values=>['Chocolate', 'Vanilla', 'Other']); 43 $form.=hr() "\n"; ... section 12.3.4). 19For additional information on creating custom modules, see Writing Perl Modules for CPAN, by Sam Tregar (Apress, 2002) Trang 20The mainstay of web programming with Perl is the CGI ... cover, this is the shorthand name used inPerl circles for the book entitled Programming Perl, which serves as the printed ref-erence manual for the Perl language classic UNIX utility Sometimes

Ngày tải lên: 06/08/2014, 03:20

... about Perl 6: Perl 5 was my rewrite of Perl I want Perl 6 to be the community’s rewrite of Perl and of the community There are several changes to the Perl language that are in the works for Perl ... James Lee Perl for those who missed it the first time around: Learn about the duct tape for the web, the cloud and system administration Beginning Covers Perl 5.10 Trang 4ii Beginning Perl, Third ... much if I never had Perl to play with Thanks also to the Perl community for all the selfless work making Perl what it is, especially Lincoln Stein for CGI.pm and Tim Bunce for DBI Lastly, thanks

Ngày tải lên: 09/08/2014, 14:21

... Trang 116 When Perl reads your program, it reads and understands numbers in any of the allowed number systems, 0 for octal, 0b for binary, and 0x for hex What happens, you might ... in line 7 before the second single quote Remember that \' tells Perl to escape the single quote, turning off its normal meaning of a closing single quote Perl continues to look for the closing ... and 15 first, and then add Which does Perl do? Try it and see Perl should give you 108, meaning it did the multiplication first The order in which Perl performs operations is called operator

Ngày tải lên: 09/08/2014, 14:21

... of the foreach (it is not available outside the looping construct) A note about the keywords for and foreach: they are synonyms for each other In other words, we We will talk more about foreach ... As before, Perl doesn’t automatically put spaces between list elements for us when it prints them out, it just prints them as it sees them Similarly, it doesn’t put a newline on the end for us2 ... as for ($i = 1; $i <= 5; $i++) { # do something important } The foreach Loop Perl has another loop called the foreach loop It is used to loop through lists and arrays We will talk about

Ngày tải lên: 09/08/2014, 14:21

... synonyms for each other. We will stick to the style of calling a foreach a foreach, but some Perl programmers call the foreach a for. This also applies to the expression modifier form of the foreach. ... Modifier for the foreach Loop Just as there was an expression modifier form of if, like this: die "Something wicked happened" if $error; there’s also an expression modifier form of foreach. ... own iterator variable: it’s always $_. It has this form: statement foreach list_or_array; Here is a quick example: #!/usr/bin/perl # foreach6.pl use warnings; use strict; my @a =

Ngày tải lên: 09/08/2014, 14:21

... word character—hence \b for boundary So, for example, to look for one-letter words: $ perl matchtest.pl Enter some text to find: \s\w\s '\s\w\s' was not found $ perl matchtest.pl Enter ... be a derogatory term for imperfectly transforming data But in the Perl culture, munge is not derogatory—being able to transform data, even if imperfectly, is one thing that Perl programmers aspire ... that =~ operator, which is !~ For example: Literal text is the simplest regular expression to look for, but we needn’t look for just the one word—we could look for any particular phrase However,

Ngày tải lên: 09/08/2014, 14:21

... does this for us in Perl: glob('*.pl') ■ Note You can perform the same action in Perl by taking the glob pattern and, like reading from a filehandle, wrap it in angle brackets Therefore, this ... value for some operations, such as print(), _ is the default filehandle for Perl’s file tests It actually refers to the last file explicitly tested Since you tested $_ previously, you can use _ for ... Except for the name of the function itself, the syntax for calling rindex() is exactly the same rindex('David Gilmour', 'i') searches from the right-hand side of “David Gilmour” looking for the

Ngày tải lên: 09/08/2014, 14:21

... For more information on these kinds of data structures, consult the Perl “Data Structures Cookbook” documentation (perldoc perldsc) or the Perl “List of Lists” documentation (perldoc perllol) ... /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl ) at /cantload.pl line 7 $ This displays ... instead of () for a hash, and [] instead of () for an array Finally, we can create a reference by creating a need for one—if a reference needs to exist for what we’re doing, Perl will bring

Ngày tải lên: 09/08/2014, 14:21

... possible that the path to Perl used in the examples: #! /usr/bin /perl will have to be changed to the location of Perl on the Windows installation, such as: #!c: /Perl/ bin /perl. exe Creating a ... performed before the object is disposed of. For instance, your FTP session object will want to ensure that it has closed the connection to the remote server. An Example It is now time for ... OBJECT-ORIENTED PERL This produces our friendly demand: $ perl utility1.pl Galileo Galilei 9 .81 Pisa Apts 4/5/2004... class is an ordinary Perl package • A method is an ordinary Perl subroutine

Ngày tải lên: 09/08/2014, 14:21

... the form The form is eventually closed with end_form() The text form widget is created with textfield(-name => 'lastname') The textfield() method is one of many methods used to create form ... information For instance, three of our performers play guitar, so any guitar data we provide we’d have to be repeat for each musician Also, several of our musicians have multiple talents—for ... program Perl offers many ways to template your web site including HTML::Template, the Template Toolkit, Mason, and Embperl Summary CGI is the cornerstone of programming for the web, and Perl

Ngày tải lên: 09/08/2014, 14:21

... appeared upon acceptance Fully formattedPDF and full text (HTML) versions will be made available soon. Healthcare utilization and costs in patients beginning pharmacotherapy for generalized anxiety ... printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central. For information about publishing your ... reproduction in any medium, provided the original work is properly cited. Trang 2Healthcare utilization and costs in patients beginning pharmacotherapy for generalized anxiety disorder: a retrospective

Ngày tải lên: 11/08/2014, 16:21

... conditional random fields Bioinformatics 2005, 21(2):237-242. 7. Wang L, Sauer UH: OnD-CRF: predicting order and disorder in proteins conditional random fields Bioinformatics 2008, 24(11):1401-1402. ... fields Bioinformatics 2007, 23(5):597-604. 10. Dang TH, Van Leemput K, Verschoren A, Laukens K: Prediction of kinase-specific phosphorylation sites using conditional ran-dom fields Bioinformatics ... multiple sources of information in conditional random fields Bioinformatics 2009, 25(11):1433-1434. 12. Wang S, Quattoni A, Morency L, Demirdjian D: Hidden Condi-tional Random Fields for Gesture Recognition

Ngày tải lên: 12/08/2014, 17:20

... SampsonPerl for Beginners Trang 3Perl for Beginners© 2010 Geoffrey Sampson & Ventus Publishing ApS ISBN 978-87-7681-623-0 Trang 4Perl for Beginners ContentsStand out from the crowd Designed for ... which conform to Trang 15Perl for Beginners Getting startedThe reason for allowing the underline character is so that it can be used to represent a written space when the obvious name for something ... command: perl twoandtwo.pl The perl command can be modified by various options beginning with hyphens, one of which is -w for “give warnings” If we ran the program using the command: perl -w twoandtwo.pl

Ngày tải lên: 22/10/2014, 20:34

... design into Perl code, you can uncomment the Perl code by removing the # signs. In this way you may have a mixture of Perl and pseudocode, but you can run and test the Perl parts; the Perl interpreter ... find, for example, web, statistics, or graphics programs. In our case, you will find the Bioperl module, which includes several useful bioinformatics functions. A module is a collection of Perl ... other places to look for already existing code. You can search the Internet with your favorite search engines. You can browse collections of links for bioinformatics, looking for programs. You...

Ngày tải lên: 15/03/2014, 17:20