Hi,
I am trying to remove duplicate lines from a file. For example the contents of example.txt is:
this is a test
2342
this is a test
34343
this is a test
43434
and i want to remove the "this is a test" lines only and end up with the numbers in the file, that is, end up with:
2342... (4 Replies)
Hi,
I need to concatenate three files in to one destination file.In this if some duplicate data occurs it should be deleted.
eg:
file1:
-----
data1 value1
data2 value2
data3 value3
file2:
-----
data1 value1
data4 value4
data5 value5
file3:
-----
data1 value1
data4 value4 (3 Replies)
Hi there, I'm new to the board and I did try a search, but couldn't quite find what I was looking for.
I deal in mostly large sets of sequential files, usually images. I was wondering if someone has modified the standard ls() command, or created another command that would display standardly... (9 Replies)
If I have a file with the following information
And I would like to remove all the sequences with Freq less than 3, so I end up having the following file:
I am currently using awk to accomplish this task but I am not getting the results I actually want.
Any help will be greatly appreciated. (3 Replies)
My file looks like this
But I need to remove the entry with the identifier >Reference1 along with the entire sequence. Thus, I will end up having the following file
Thanks in advance! (2 Replies)
Hai,
How to remove the repeated 'Chr's in different sequences. In the given example, Chr19 is repeated in two samples
with the same number i.e. +52245923. How to remove one of the entry in any of the samples and to give the range for each
Chr which is -20 for minimum range value and +120 for... (1 Reply)
Hi everybody
I have a .txt file that contains some assembly code for optimizing it i need to remove some replicated parts.
for example I have:e_li r0,-1
e_li r25,-1
e_lis r25,0000
add r31, r31 ,r0
e_li r28,-1
e_lis r28,0000
add r31, r31 ,r0
e_li r28,-1 ... (3 Replies)
Hello friends,
Could anyone please advise on how to remove escape sequences from a text file?
$ file input.txt
input.txt: ASCII English text, with escape sequences
I'm able to see those escape characters when opened in vi editor like shown below:
^
but not when I run more... (6 Replies)
Discussion started by: magnus29
6 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)