Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Tricky task with DNA sequences.

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Tricky task with DNA sequences.
# 8  
Old 09-01-2011
I think they are included in the output:


Code:
zsh-4.3.12[t]% cat infile 
>Influenza
TGGATATGAT
>Dengue
AGTTACTCCGAAA
>Varicella
CTTTGGATA
zsh-4.3.12[t]% perl -nle'BEGIN {
quote>   @map{ A, C, G, T } = ( T, G, C, A )
quote>   }
quote>   print /^>/ ?
quote>     $_ :
quote>       join //, map $map{ $_ }, split //, scalar reverse
quote>   ' infile
>Influenza
ATCATATCCA
>Dengue
TTTCGGAGTAACT
>Varicella
TATCCAAAG


Am I missing something?
This User Gave Thanks to radoulov For This Post:
Xterra
# 9  
Old 09-01-2011
This is the output I am getting
Quote:
[Virus@localhost Testing]$ perl -nle'BEGIN {
> @map{ A, C, G, T } = ( T, G, C, A )
> }
> print /^>/ ?
> $_ :
> join //, map $map{ $_ }, split //, scalar reverse
> ' infile
>Influenza
ATCATATCCA

TTTCGGAGTAACT

TATCCAAAG
[Virus@localhost Testing]$
Now I am not sure, I am missing something?

---------- Post updated at 10:13 AM ---------- Previous update was at 10:12 AM ----------

Input file was not the correct one!
It is working like a charm!
Thanks!
Login or Register to Ask a Question

Previous Thread | Next Thread

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Convert a DNA sequence into Amino Acid

I am trying to write a bash script that would be able to read DNA sequences (each line in the file is a sequence) from a file, where sequences are separated by an empty line. I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals.) For example, if I... (3 Replies)
Discussion started by: faizlo
3 Replies

2. 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

3. HP-UX

Tricky situation getting IP address

Hi, I have a multihomed system HP-UX with two NIC cards having IP address 10.9.0.13 & 10.9.0.45 I have two weblogic servers running one listening on "10.9.0.13" and the other on "10.9.0.45" Given a PID how is it possible to extract the IP Address that the weblogic server is using and... (1 Reply)
Discussion started by: mohtashims
1 Replies

4. Solaris

Tricky egrep

Hi folks! My first post here. I'm working on a script that retrieves a range of files from a list depending on a range of time. UPDATE: I've seen it could be difficult to read all this thing, so I'll make a summarize it.. How come I do this and take a result.. grep "..\:.." lista.new |... (4 Replies)
Discussion started by: kl0x
4 Replies

5. 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

6. Shell Programming and Scripting

Parse an XML task list to create each task.xml file

I have an task definition listing xml file that contains a list of tasks such as <TASKLIST <TASK definition="Completion date" id="Taskname1" Some other <CODE name="Code12" <Parameter pname="Dog" input="5.6" units="feet" etc /Parameter> <Parameter... (3 Replies)
Discussion started by: MissI
3 Replies

7. Shell Programming and Scripting

comment and Uncomment single task out of multiple task

I have a file contains TASK gsnmpproxy { CommandLine = $SMCHOME/bin/gsnmpProxy.exe } TASK gsnmpdbgui { CommandLine = $SMCHOME/bin/gsnmpdbgui.exe I would like to comment and than uncomment specific task eg TASK gsnmpproxy Pls suggest how to do in shell script (9 Replies)
Discussion started by: madhusmita
9 Replies

8. Shell Programming and Scripting

Tricky Sed

Hello. I am trying to convert occurrences of 'NULL' from a datafile. The 'NULL' occurences appears at this: |NULL| NULL|NULL| NULL|NULL| NULL|NULL| NULL| There should be 52 fields per line. I would like any occurrence of | NULL| or |NULL| to appear as '||' Currently I am using this sed... (2 Replies)
Discussion started by: bestbuyernc
2 Replies

9. Windows & DOS: Issues & Discussions

Tricky one...

Here's my problem: I have a laptop running Windows XP Pro with no internal CD or Floppy drives. I want to install Linux on it. I don't care about the Windows XP Pro installation, in fact I would like to install Linux over the entirety of the HD. However I cannot boot from any external CD drive... (1 Reply)
Discussion started by: saabir
1 Replies
Login or Register to Ask a Question