Sponsored Content
Top Forums Shell Programming and Scripting Convert a DNA sequence into Amino Acid Post 302957300 by faizlo on Thursday 8th of October 2015 06:50:02 PM
Old 10-08-2015
Here is what I did:
  • Created a file dna.sed
  • Created another bash script file with your code (starting with the usual #!)
  • Called the shell script "conversion.sh" and chmod it to excutable
  • ran it like this: ./conversion.sh < dna_input.dna
  • Got my result as expected for the test input file.
Thank you for your help.
How would one put this into a single script file?
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

escape sequence for $

Hi all, I have a requirement where the variable name starts with $, like $Amd=/home/student/test/ How to work wit it? can some one help me, am in gr8 confusion:confused: (5 Replies)
Discussion started by: shreekrishnagd
5 Replies

2. Shell Programming and Scripting

How to remove those sequence with same amino acid?What command line I should type?

My input is listed as: giNumber RefAminoAcid VarAminoAcid 10190711 P P 10190711 D D 109255248 I A 110349771 A ... (4 Replies)
Discussion started by: patrick chia
4 Replies

3. Shell Programming and Scripting

Extracting DNA sequences from GenBank files using Perl

Hi all, Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here... Nucleotide This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
Discussion started by: akreibich07
5 Replies

4. Shell Programming and Scripting

Tricky task with DNA sequences.

I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this: Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted... (8 Replies)
Discussion started by: Xterra
8 Replies

5. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

6. Shell Programming and Scripting

How to convert multiple number ranges into sequence?

Looking for a simple way to convert ranges to a numerical sequence that would assign the original value of the range to the individual numbers that are on the range. Thank you given data 13196-13199 0 13200 4 13201 10 13202-13207 3 13208-13210 7 desired... (3 Replies)
Discussion started by: jcue25
3 Replies

7. Shell Programming and Scripting

Sequence generator

Thanks Guys This really helped (5 Replies)
Discussion started by: robert89
5 Replies

8. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies

9. Red Hat

Rm -rf * sequence

If I run rm -rf * command under one parent directory. /data > rm -rf * Is there anyway to know which files will be deleted first ? Start using code tags please, ty. (2 Replies)
Discussion started by: sameermohite
2 Replies
EXIM_CONVERT4R4(8)					      System Manager's Manual						EXIM_CONVERT4R4(8)

NAME
exim_convert4r4 - Convert Exim configuration from v3 to v4 format SYNOPSIS
exim_convert4r4 DESCRIPTION
This script is provided to assist in updating Exim configuration files. It reads an Exim 3 configuration file on the standard input, and writes a modified file on the standard output. It also writes comments about what it has done to the standard error file. It assumes that the input is a valid Exim 3 configuration file. A typical call to the conversion script might be exim_convert4r4 < /etc/exim/exim.conf > /etc/exim4/exim4.conf.new The output file MUST be checked and tested before trying to use it on a live system. The conversion script is just an aid which does a lot of the "grunt work". It does not guarantee to produce an Exim 4 configuration that behaves exactly the same as the Exim 3 configuration it reads. Each option change in the new file is preceded by an identifying comment. In fact, the conversion script tends to make quite a mess of your configuration, and you should expect to go through it afterwards and tidy it up by hand. Unless you are running a very straightforward configuration, the automatic conversion is likely to generate a non-optimal configuration. You should not only check it thoroughly, but also run as many tests as you can, to ensure that it is working as you expect. In particular, you should test address routing, using -bt and -bv, and the policy controls, using -bh. If possible, you should also do some live tests (i.e. send and receive some messages) before putting Exim 4 into service. If you have a very complicated configuration, it is possible that exim_convert4r4 will break it in some situations, which is why thorough testing is strongly recommended. BUGS
This manual page needs a major re-work. If somebody knows better groff than us and has more experience in writing manual pages, any patches would be greatly appreciated. SEE ALSO
exim(8), the files in /usr/share/doc/exim4-base/, especially Exim4.upgrade.gz AUTHOR
This manual page was stitched together from Exim4.upgrade by Andreas Metzler <ametzler at downhill.at.eu.org>, for the Debian GNU/Linux system (but may be used by others). March 26, 2003 EXIM_CONVERT4R4(8)
All times are GMT -4. The time now is 02:49 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy