07-17-2011
Substitute string using location (preferably perl).
I have a string like.
ATATATATTATTATATTATATTATT
I want to substitute the characters to "C" by using these locations
3 7
10 18
15 20
desired Output:
ATCCCCCTTACCCCCCCCCCTTATT
any clue will be great help.
thanks in advance.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hi guys,
with sed when I need to make a substitution inside a line containing a specific keyword, I usually use:
sed '/keyword/ s/cat/dog/g'
This will substitute "cat" with "dog" on those lines containing "keyword". Now I want to use this inside vi, for several reason that I cannot... (2 Replies)
Discussion started by: lycaon
2 Replies
2. Shell Programming and Scripting
Suppose,
d=ABC*.BGH.LKJ
Now I want to replace 'DEFGHIJ' instead of '*.B' and store the value in d. Any Idea? Can we use sed here?
The outout should be like this:
d=ABCDEFGHIJGH.LKJ
Please help.. (4 Replies)
Discussion started by: Niroj
4 Replies
3. Shell Programming and Scripting
Hi,
I have a string like this user can specify different query sets that is why "or" is mentioned:
$string="](";
or
$string="]((";
or
$string="](((";
or
$string="]((((("; (1 Reply)
Discussion started by: vanitham
1 Replies
4. Shell Programming and Scripting
Hi Everyone,
I have 1.txt
here
a
b
c' funny"yes";
d
e
The finally output is:
here
a
b
c
d
e' funny"yes"; (1 Reply)
Discussion started by: jimmy_y
1 Replies
5. Shell Programming and Scripting
I am having trouble with a part of my substitute script I am using. I have it look through a file and find an exact match and then if it finds that match in the 1 file it should run the following 1 liner on 3 different files.
perl -pi -e 's/$CurrentName\s/$NewName/g' foo.cfg;
The issue that is... (8 Replies)
Discussion started by: Takau
8 Replies
6. UNIX for Dummies Questions & Answers
Hi,
I started exploring unix recently. Now i have got a requirement like i have a input file where i am having some strings line by line (One string Might be single line or multiple lines). Now i need find these strings in another file and if its found i have to replace it with another string... (2 Replies)
Discussion started by: Sivajee
2 Replies
7. Shell Programming and Scripting
Objective is to substitute Jan with 01, Feb with 02 and so on. The month will be provided as input.
I could construct below awk and it worked.
echo Jun | \
awk 'BEGIN{split("Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec",mon," ")}{ for (i=1;i<=12;i++){ if ($1==mon) printf("%02d\n",i)} }'
... (4 Replies)
Discussion started by: krishmaths
4 Replies
8. Shell Programming and Scripting
Hi
I have 3 files in total. file 1 is enriched.txt file2 is repressed.txt and file 3 is my content.txt
What i need is query the content file against both enriched and repressed and wherever the gensymbol is same in both the files then add a yes value against it
file1
Gene
ABC
XYZ
MNO... (12 Replies)
Discussion started by: Diya123
12 Replies
9. Shell Programming and Scripting
Dear all,
I try to replace a string of characters in a file (MyFile.txt) by a multiline value of the variable "Myvar":
$ cat MyFile.txt
DESCRIPTION '@TargetTable SCHEMA'
(
@InputFlowDef
);
$
The content of Myvar:
$ echo "$Myvar"
col1
, col2
, col3
$ (4 Replies)
Discussion started by: dae
4 Replies
10. UNIX for Beginners Questions & Answers
I want to search a small string in a large string and find the locations of the string. For this I used grep "string" -ob <file name where the large string is stored>. Now this gives me the locations of that string. Now how do I store these locations in a text file.
Please use CODE tags as... (7 Replies)
Discussion started by: ANKIT ROY
7 Replies
LEARN ABOUT DEBIAN
bio::factory::locationfactoryi
Bio::Factory::LocationFactoryI(3pm) User Contributed Perl Documentation Bio::Factory::LocationFactoryI(3pm)
NAME
Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string
SYNOPSIS
# Do not use directly, see Bio::Factory::LocationFactory for example
use Bio::Factory::FTLocationFactory;
my $locfact = Bio::Factory::FTLocationFactory->new();
my $location = $locfact->from_string("1..200");
print $location->start(), " ", $location->end(), " ", $location->strand,"
";
DESCRIPTION
An interface for Location Factories which generate Bio::LocationI objects from a string.
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 - Hilmar Lapp
Email hlapp at gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
from_string
Title : from_string
Usage : $loc = $locfactory->from_string("100..200");
Function: Parses the given string and returns a Bio::LocationI implementing
object representing the location encoded by the string.
Different implementations may support different encodings. An
example of a commonly used encoding is the Genbank feature table
encoding of locations.
Example :
Returns : A Bio::LocationI implementing object.
Args : A string.
perl v5.14.2 2012-03-02 Bio::Factory::LocationFactoryI(3pm)