Hi All,
I have a file that I need to be able to find a pattern match on a line, search that line for a text pattern, and replace that text.
An example of 4 lines in my file is:
1. MatchText_randomNumberOfText moreData ReplaceMe moreData
2. MatchText_randomNumberOfText moreData moreData... (4 Replies)
I have a text file with following content (3 lines)
filename : output.txt
first line:12/12/2008
second line:12/12/2008
third line:Y
I would like to know how we can replace 'Y' with 'N' in the 3rd line keeping 1st and 2nd lines same as what it was before.
I tried using cat output.txt... (4 Replies)
Hi,
I wanted to add a newline character after every 100 characters in a file using a awk or shell without reading each line of the file.
I want to run a command on the complete file.
This does based on a string but i want to add a new line after every 100 characters ir-respective of the... (3 Replies)
Need to replace any control character in the string in perl
---------- Post updated at 04:22 PM ---------- Previous update was at 03:50 PM ----------
Any help !!!
Thanks in advance (2 Replies)
Hello,
I am trying to search and replace but I don't know how to do it. My simple knowlegde in search and replace using sed is not helping me at all.
File:
its a cause value #22: dfg ggg
Cause value #1: aasfa fasdf
asfa value #22: affg gggg
Basically i want to replace the... (6 Replies)
Hi All,
We are getting an external file in abc.csv format. When opened in excel spread sheet, it is opening alright. But when opened in notepad, I see the contents in a single line.
Ftp'd the file in binary mode to AIX UNIX host. When opened, I see Control M (^M) characters in place of New Line... (16 Replies)
Hi Unix gurus,
I've a dna sequence in a file format known as fasta format (sequence header starts with > and ignored), an example shown below:
>sequence_1
CGTATTCTCCGAATACC
ATACG
>sequence_2
CAGATTTTCAAATACCCCC
In a file like this I want to do the following three search and replace. The... (4 Replies)
This is for AIX 6.1, I've a flat file and the format is like this
DECLARE
some statements;
BEGIN
some statements;
END;
I've to search BEGIN and replace it with the following 4 lines
BEGIN
For x in 1..1
LOOP
BEGIN
Similarly I've to search END and replace it with the... (7 Replies)
Discussion started by: Mukul Sharma
7 Replies
10. Post Here to Contact Site Administrators and Moderators
In file, we have millions of records each of 1000 in length. And at specific position say 800 there is a space, we need to replace it with Character X if the ID in that row starts with 123.
So far i have used the below which is replacing space at that position to X but its not checking for... (3 Replies)
Discussion started by: Jagmeet Singh
3 Replies
LEARN ABOUT DEBIAN
bio::factory::treefactoryi
Bio::Factory::TreeFactoryI(3pm) User Contributed Perl Documentation Bio::Factory::TreeFactoryI(3pm)NAME
Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
from/to a data stream
SYNOPSIS
# get a $factory from somewhere Bio::TreeIO likely
my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
-file => 'file.tre');
my $treeout = Bio::TreeIO->new(-format => 'nexus',
-file => ">file.nexus");
# convert tree formats from newick/phylip to nexus
while(my $tree = $treeio->next_tree) {
$treeout->write_tree($tree);
}
DESCRIPTION
This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO
factory.
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 the
Bioperl mailing list. 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 of 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@bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_tree
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get a tree from the factory
Returns : L<Bio::Tree::TreeI>
Args : none
write_tree
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : L<Bio::Tree::TreeI>
perl v5.14.2 2012-03-02 Bio::Factory::TreeFactoryI(3pm)