the problem is, that "let" can`t define the variable, as variable looks like "/portal/ticket/show/090107-01666?status=open".
as you can see script should define a number of line(1-x) variables and echo them
Could you please suggest some options?
Hi All,
I have been trying to set variable environment for the JAVA_HOME but it doesn' work. The path set is as follows
setenv JAVA_HOME "/usr/local/jdk1.3"
setenv PATH $JAVA_HOME/bin
setenv CLASSPATH ${JAVA_HOME}/lib/tools.jar:{JAVA_HOME}/lib/dt.jar
can anyone suggest Me where am I and... (2 Replies)
I have some function
function()
{
fileNamelist=( `find Uploads -name "somePattern" | tr '\n' ' '` )
}
but "local fileNamelist" makes it variable.
How do I declare fileNameList as a local array in BASH? (1 Reply)
Hi all,
It might seem like a very trivial question but I am new to shell scripting so excuse for that.
I have an existing script in CSH. I need to create a function in the script which takes some parameters and returns a result. Can someone please let me know the syntax for function... (4 Replies)
Hi all. Im trying to use a sequence in a while loop like this below. I need it for navigating a year, month, day folder structure where a user can input the start date and have it go to the desired end date. The script will grab a certain file on each day then move onto the next. Ive got all that... (3 Replies)
Hey guys im facing a problem in declaring variables. i have a few classes like the one below...
#ifndef _FINANCE_H
#define _FINANCE_H
#include <string>
#include <iostream>
#include <fstream>
#include <stdlib.h>
using namespace std ;
class readStraitsTimesIndex
{
... (3 Replies)
I usually just browse the forum/google for answers, however I've been stuck on a problem for a number of hours now and I've decided to join up and actually ask I've searched the forum ad naseum in an attempt to find answer to my query, however so far I have been unsuccessful.
I'm no expert... (3 Replies)
Hi All,
The issue is that for changing name of the file i'm writing a script, there the at one point i need to declare a variable some thing like 'var1, var2, var3 ......' which has to store some value.
Script as follows:
for i in `echo xxxx_dddd_ccc_plsql_zz.sql |tr "_" ' '`
do
... (2 Replies)
I get an error in my shell script that line 1: )unexpected.
Line 1 in my script (using sh by the way) is the variable I declared but did not initialize it.
result=
Is this wrong? How can I fix it? I am using the variable later in the program, so I figured I could just declare it first... (4 Replies)
Is it possible to declare an array in the following way:
@tmp = (@f,"String1","String2", "String3",@f);
I'm getting the following error message:
Array found where operator expected at Program.pl line 181, near ""
(Missing semicolon on previous line?)
---------- Post updated at... (1 Reply)
Does anyone know how to declare an array in csh? I don't want to declare any elements in the array because I have a variable that represents the size of the array. For example: the array I want to declare is called sortList and it passes in the variable ARRAYSIZE that stores the value 8. (1 Reply)
Discussion started by: demet8
1 Replies
LEARN ABOUT DEBIAN
bio::seqio::kegg
Bio::SeqIO::kegg(3pm) User Contributed Perl Documentation Bio::SeqIO::kegg(3pm)NAME
Bio::SeqIO::kegg - KEGG sequence input/output stream
SYNOPSIS
# It is probably best not to use this object directly, but
# rather go through the SeqIO handler system. Go:
use Bio::SeqIO;
$stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
DESCRIPTION
This class transforms KEGG gene records into Bio::Seq objects.
Mapping of record properties to object properties
This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It
is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the
Bio::Seq::RichSeqI implementing object returned by the parser for each record.
'ENTRY'
$seq->primary_id
'NAME'
$seq->display_id
'DEFINITION'
$seq->annotation->get_Annotations('description');
'ORTHOLOG'
grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink')
'CLASS'
grep {$_->database eq 'PATH'}
$seq->annotation->get_Annotations('dblink')
'POSITION'
FIXME, NOT IMPLEMENTED
'PATHWAY'
for my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
#
}
'DBLINKS'
$seq->annotation->get_Annotations('dblink')
'CODON_USAGE'
FIXME, NOT IMPLEMENTED
'AASEQ'
$seq->translate->seq
'NTSEQ'
$seq-E<gt>seq
FEEDBACK
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 - Allen Day
Email allenday@ucla.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq::RichSeq object
Args :
write_seq
Title : write_seq
Note : write_seq() is not implemented for KEGG format output.
perl v5.14.2 2012-03-02 Bio::SeqIO::kegg(3pm)