This should read $ARGV[0] etc. instead. If you have the -w flag on, it will give you a warning. And I don't think you need a chomp() on command line arguments anyway.
Putting a pair of quotes around the value is required by the shell. You can probably workaround it by
$split_val = join(' ', @ARGV[1..(@ARGV-1)]);
to have Perl absorbs all command line parameters delimited by whitespace and glues them into a single string, but the reconstructed string may not be identical to the original string you intended to get. Who says that one space is always the delimiter? For instance by giving the following as command line arguments
Note the two spaces between a and b, which are treated as one whitespace delimiter by the shell and the code above transforms it to (thus the value of $split_val)
This arrangement is probably okay if the arguments are like a composite command, and whitespace is not significant. But literally, the string has been modified, and this is unlikely to be what you want.
I've written a script (bgrep) for a more advanced grep command (& attached a cut down version below). I'm trying allow all grep options to be used, or in any combination.
The script works fine if I type say
bgrep -i -files product
it will return a non-case sensitive list of matches for... (3 Replies)
All,
I have a cron job script that receives several command line arguments. At some point if there are validation problems and the job cannot be run, it duplicates the entire command line into a temporary text file which is later executed as a script. Unfortunately when I pass the list of received... (7 Replies)
Hi,
I am writing a script, which is invoked from other system using ssh.
I have problems reading the arguments passing to the script. If the argument has a space in it (ex "rev 2.00"), the script considers "rev" as 1 argument and "2.00" as another. Instead i want "rev 2.00" to be considered... (5 Replies)
Hi All,
I am trying to pass an argument called "Pricelist" to a Perl function, then the function will open and print out the contents of the file named "Pricelist". But i can't seem to do it using my below code. Can any expert give some advice?
#!/usr/local/bin/perl
$DATABASE =... (1 Reply)
Hi Gurus,
i have one requirement in unix script, i have a file called abc.txt in that few lines are there with the empid, i need to read each line and pass to .sql script.
ex:
abc.txt
2345
2346
1243
1234
i need to pass these arguments to .sql script rom unix
ex:
select * from... (1 Reply)
Hi!
I have a python script that requires arguments and these arguments are file paths. This script works fine when executed like this:
/my_python_script "file_path1" "file_path2"
(i added quotes as some file names may have weird characters)
the issue happens when i launch my python script... (14 Replies)
Hi I need to pass comma seperated arguments to a perl script?
It is like:
Exect.pl -d GUI1,GUI2,GUI3
and I need to store these argsGUI1,GUI2,GUI3 in an array.
can anyone suggest how to do that: (1 Reply)
Semi-newbie, so flame throwers to 'singe-only', please. ;-)
I have a large number of (say) .html files, where I'd like to do a recursive in-place search and replace a particular string. The following bit of perl works fine:
perl -pi -e 's/oldstring/newstring/g' `find ./ -name *.html`
... (2 Replies)
Hi,
I wanted to pass an argument to a bash script. So that the argument is used inside the awk command inside the bash script.
I know the noraml way of passing argument to a bash script as below :
sh myScript.sh abc
Inside the bash script i can use like this
myArg1=$1
wc $myArg
But... (8 Replies)
Hi,
I have a requirement for creating a MQ (queue) where the inputs has to be passed as arguments.
Running the script as below
./hi.sh "Servername" "QueueManagername" "QueuecreationCommand"
cat hi.sh
echo "Welcome to $1"
runmqsc $2 < $3
But the queue creation command is... (9 Replies)
Discussion started by: Anusha M
9 Replies
LEARN ABOUT DEBIAN
bio::index::fasta
Bio::Index::Fasta(3pm) User Contributed Perl Documentation Bio::Index::Fasta(3pm)NAME
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
SYNOPSIS
# Make an index for one or more fasta files
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Once the index is made it can accessed, either in the
# same script or a different one
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',
-fh => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq object
$out->write_seq($seq);
}
# or, alternatively
my $id;
my $seq = $inx->get_Seq_by_id($id); # identical to fetch()
DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fasta files, and
retrieving the sequence from them. For best results 'use strict'.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
Additional example code is available in scripts/index/*PLS and in the Bioperl Tutorial (<http://www.bioperl.org/wiki/Bptutorial.pl>)
Note that by default the key for the sequence will be the first continuous string after the '>' in the fasta header. If you want to use a
specific substring of the fasta header you must use the id_parser() method.
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
$inx->make_index($file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /^>.+gi|(d+)/;
$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 - James Gilbert
Email - jgrg@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_file_format
Title : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fasta'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTA 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. Useful
for (for instance) specifying a different
parser for different flavours of FASTA file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
description line. 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( $header )
Function: The default Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fasta header line string
perl v5.14.2 2012-03-02 Bio::Index::Fasta(3pm)