Search for a particular word and replace the first character
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:
In a file like this I want to do the following three search and replace. The original file becomes three different files based on each search condition.
1) search two character pattern CG and replace that C by the word NULL
2) search three character pattern CXG and replace that C by the word NULL (where X=A,C or T but not G)
3) search three character pattern CXX and replace that C by the word NULL (where X=A,C or T but not G)
Example output based on above file:
File_CG_replace
File_CXG_replace
File_CXX_replace
Thanks for your help.
Hi
I would like to accept in a string from user like
username/pwd@dbname
suppose the user does not input @ then i should throw an error that @ symbol missing . How to achieve this
Thanks in advance
Suresh (6 Replies)
Hi,
I am trying to write a shell script designed to take input line by line by line from a file with a word on each line for editing with sed. Example file:
1.ejverything
2.bllown
3.maikling
4.manegement
5.existjing
6.systems
My design currently takes input from the user, and... (2 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)
Greetings,
Using vi, how can I change the following text:
-I/myviews/nexus_7400rel/vobs/nexus/platforms/97400/include -I/myviews/nexus_7400rel/vobs/nexus/modules/i2c/7400/include -I/myviews/nexus_7400rel/vobs/nexus/modules/surface/7400/include
Into this:... (4 Replies)
Hi Guys,
Req your help in searching and replacing the word that comes after equals(=) symbol
I would like to replace the sting in bold with a string in variable.
d=ABCDF8C44C22
# grep -i NIM_MASTERID ${_NIMINFO}
export NIM_MASTERID=00CDF8C44C00
I'm looking to replace any word that... (4 Replies)
Hello Unix Users,
I am very new to Unix so I am not sure how do I do the following.
I need a script such that when I type the following in the command prompt
> . scriptName.sh wordToBeReplaced DirectoryLocation
will find the word someword located in a somefile.xml in DirectoryLocation... (8 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)
Hi All
i need to replace the url1 inside <remote> tag in below xml in first instance and in the second instance with url2.
any help appreciated
<locations>
<hudson.scm.SubversionSCM_-ModuleLocation>
<remote>https://svn2015.com/svn/repos/internalshard</remote>
... (4 Replies)
Discussion started by: madankumar.t@hp
4 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
kalign
KALIGN(1) Kalign User Manual KALIGN(1)NAME
kalign - performs multiple alignment of biological sequences.
SYNOPSIS
kalign [infile.fasta] [outfile.fasta] [Options]
kalign [-i infile.fasta] [-o outfile.fasta] [Options]
kalign [< infile.fasta] [> outfile.fasta] [Options]
DESCRIPTION
Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
alignment.
OPTIONS -s -gpo -gapopen -gap_open x
Gap open penalty .
-e -gpe -gap_ext -gapextension x
Gap extension penalty.
-t -tgpe -terminal_gap_extension_penalty x
Terminal gap penalties.
-m -bonus -matrix_bonus x
A constant added to the substitution matrix.
-c -sort <input, tree, gaps.>
The order in which the sequences appear in the output alignment.
-g -feature
Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?
-same_feature_score
Score for aligning same features.
-diff_feature_score
Penalty for aligning different features.
-d -distance <wu, pair>
Distance method
-b -tree -guide-tree <nj, upgma>
Guide tree method.
-z -zcutoff
Parameter used in the wu-manber based distance calculation.
-i -in -input
Name of the input file.
-o -out -output
Name of the output file.
-a -gap_inc
Increases gap penalties depending on the number of existing gaps.
-f -format <fasta, msf, aln, clu, macsim>
The output format.
-q -quiet
Print nothing to STDERR. Read nothing from STDIN.
REFERENCES
o Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
6:298
o Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
sequences allowing external features. Nucleic Acid Research 3:858?865.
AUTHORS
Timo Lassmann <timolassmann@gmail.com>
Upstream author of Kalign.
Charles Plessy <plessy@debian.org>
Wrote the manpage.
COPYRIGHT
Copyright (C) 2004, 2005, 2006, 2007, 2008 Timo Lassmann
Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the
Free Software Foundation.
This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under the same terms as kalign itself.
On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2.
kalign 2.04 February 25, 2009 KALIGN(1)