Hi
My orginal file is like (100s of lines)
id host ip location remarks
1 host1 ip1 - xxx
2 host2 ip2 - xxx
3 host3 ip3 - xxx
--
--
9 host9 ip9 - xxx
I have a ref file like
host1 location1
host2 location2
host3 location3
--
--... (6 Replies)
using sed to replace a specific string on a specific line number using variables
this is where i am at
grep -v WARNING output | grep -v spawn | grep -v Passphrase | grep -v Authentication | grep -v '/sbin/tfadmin netguard -C'| grep -v 'NETWORK>' >> output.clean
grep -n Destination... (2 Replies)
I am trying to use sed to replace specific characters at a specific position in the file with a different value... can this be done?
Example:
File:
A0199999123
A0199999124
A0199999125
Need to replace 99999 in positions 3-7 with 88888.
Any help is appreciated. (5 Replies)
hello,
i 'd like your help about a bash script which:
1. finds inside the html file (it is attached with my post) the code number of the Latest Stable Kernel,
2.finds the link which leads to the download location of the Latest Stable Kernel version,
(the right link should lead to the file... (3 Replies)
I'm trying to update a text file via sed/awk, after a lot of searching I still can't find a code snippet that I can get to work.
Brief overview:
I have user input a line to a variable, I then find a specific value in this line 10th field in this case. After asking for new input and doing some... (14 Replies)
Hello,
I would like to change my setting in a file to the setting that user input.
For example, by default it is
ONBOOT=ON
When user key in "YES", it would be
ONBOOT=YES
--------------
This code only adds in the entire user input, but didn't replace it.
How do i go about... (5 Replies)
I have the file like this.
cat 123.txt
<p> <table border='1' width='90%' align='center' summary='Script output'> <tr><td>text </td> </tr> </table> </p>
I want to replace some tags and want the output like below. I tried with awk & sed commands. But no luck. Could someone help me on this?
... (4 Replies)
Hi,
I have a file with hundreds of lines. I want to search for particular lines starting with 4000, search and replace the 137-139 position characters; which will be '000', with '036'. Can all of this be done without opening a temp file and then moving that temp file to the original file name.
... (7 Replies)
Hi All,
I need one help to replace particular words in file based on if finds another words in that file .
i.e.
my self is peter@king.
i am staying at north sydney.
we all are peter@king.
How to replace peter to sham if it finds @king in any line of that file.
Please help me... (8 Replies)
Discussion started by: Rajib Podder
8 Replies
LEARN ABOUT DEBIAN
bio::tools::grail
Bio::Tools::Grail(3pm) User Contributed Perl Documentation Bio::Tools::Grail(3pm)NAME
Bio::Tools::Grail - Results of one Grail run
SYNOPSIS
$grail = Bio::Tools::Grail->new(-file => 'result.grail');
# filehandle:
$grail = Bio::Tools::Grail->new( -fh => *INPUT );
# parse the results
while($gene = $grail->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene
# $gene->exons() returns an array of
# Bio::Tools::Prediction::Exon objects
# all exons:
@exon_arr = $gene->exons();
# initial exons only
@init_exons = $gene->exons('Initial');
# internal exons only
@intrl_exons = $gene->exons('Internal');
# terminal exons only
@term_exons = $gene->exons('Terminal');
# singleton exons only -- should be same as $gene->exons() because
# there are no other exons supposed to exist in this structure
@single_exons = $gene->exons('Single');
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$genscan->close();
DESCRIPTION
The Grail module provides a parser for Grail gene structure prediction output.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_prediction
Title : next_prediction
Usage : while($gene = $grail->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Grail result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
_parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cds
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
perl v5.14.2 2012-03-02 Bio::Tools::Grail(3pm)