hi all
i was going through some perl code i came across this line and i am not getting what is exactly going on ..
$$this{localtion} = GetName->GetVarName("EXE_DIR") ;
what is the red part doing in above code (2 Replies)
All,
Does it matter what perl verios your running when you get syntax errors?
on version 5.6.1 the code works fine, but on 5.8.0 the code gets errors?
#!/usr/bin/perl
#use strict;
#use warnings;
my $mess = 'messages';
my $mess1 = 'messages.1';
my $mess2 = 'messages.2';
my... (13 Replies)
Hi,
I am a newbie to PERL and working on a script. When running it I get a lot of compilation errors.
The actual command in the program (which is within a case structure) is given below
# This gives the actual count of inquires from a log file (It works fine when I type this on the... (2 Replies)
I'm just trying to confirm that I understand someone's code correctly.
If someone has code that says:
$foo ||= mysub();
I'm assuming that it means if $foo is nothing or undef, then assign it some value via mysub(). If I'm wrong on this, please let me know.
Also, what's the difference... (4 Replies)
Hi,
i am running this code but i am getting syntax error
#!/usr/bin/perl
use warnings;
use strict;
use XML::LibXML;
use XML::LibXML::Reader;
use Data::Dumper;
my $file;
open( $file, 'DTC_Specification_transformed.xml');
my $reader = XML::LibXML::Reader->new( IO => $file ) or die... (1 Reply)
Hallo everybody,
I have a following problem - I'm doing a map funciont to fill in a HTML table and I want to use some radiobutton groups. Unfortunatelly, they are grouped by names, so I have to add some "counter" that will divide one row from another, and I'm using CGI.pm for generating the... (3 Replies)
Query with perl syntax
Aim: is to change a perl script to use a new file
I was required to replace
- entries \"$entries\"
with
-lib <full_path_to_filename>
So in the code detector.pm
sub rundetector
{
my $class = shift;
mkdir($resultDirectory);
my... (3 Replies)
Greetings!
Here's what I believe is a "simple one" for the community tonight ;)
What I'm trying to do is assign a "true/false" value to a variable depending upon whether a named process (some-process) exists; and then test for this value in the succeeding logic. I banged my head against the... (2 Replies)
Discussion started by: LinQ
2 Replies
LEARN ABOUT DEBIAN
bio::index::swissprot
Bio::Index::Swissprot(3pm) User Contributed Perl Documentation Bio::Index::Swissprot(3pm)NAME
Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.
SYNOPSIS
# Make an index for one or more Swissprot files:
use Bio::Index::Swissprot;
use strict;
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(
-filename => $index_file_name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index in Genbank
# format:
use Bio::Index::Swissprot;
use Bio::SeqIO;
use strict;
my $out = Bio::SeqIO->new( -format => 'genbank',
-fh => *STDOUT );
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns a Bio::Seq object
$out->write_seq($seq);
}
# alternatively
my ($id, $acc);
my $seq1 = $inx->get_Seq_by_id($id);
my $seq2 = $inx->get_Seq_by_acc($acc);
DESCRIPTION
By default the index that is created uses the AC and ID identifiers as keys. This module inherits functions for managing dbm files from
Bio::Index::Abstract.pm, and provides the basic functionality for indexing Swissprot files and retrieving Sequence objects from them. For
best results 'use strict'.
You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For
example:
$inx->id_parser(&get_id);
# make the index
$inx->make_index($index_file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /^KWs+([A-Z]+)/i;
$1;
}
FEED_BACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Also lorenz@ist.org, bosborne at alum.mit.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index Swissprot format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string.
Returns &default_id_parser (see below) if not
set. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $line )
Function: The default parser for Swissprot.pm
Returns $1 from applying the regexp /^IDs*(S+)/
or /^ACs+([A-Z0-9]+)/ to the current line.
Returns : ID string
Args : a line string
_file_format
Title : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Index::Swissprot(3pm)