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

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# 1  
Old 12-30-2013
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 "mydesired_name_45" replacing serially 46,47, 48 with my desired name as static next to each of the > symbol.

kindly help me with the script
# 2  
Old 12-30-2013
Welcome to Forum.

How do you expect output ? Like this ?

Input file :
Code:
$ cat fasta_file
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat

Code to run on terminal :
Code:
$ awk '(/^>/ && sub(/>.*_/,">"new)) + 1' new="mydesired_name_" fasta_file

Resulting :
Code:
>mydesired_name_45
atatagcaga
>mydesired_name_46
atatagcagaatatatat

This User Gave Thanks to Akshay Hegde For This Post:
margarita
# 3  
Old 12-30-2013
Code:
sed 's/>admin_1_/>mydesired_name_/' filename

# 4  
Old 12-30-2013
Quote:
Originally Posted by Akshay Hegde
Welcome to Forum.

How do you expect output ? Like this ?

Input file :
Code:
$ cat fasta_file
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat

Code to run on terminal :
Code:
$ awk '(/^>/ && sub(/>.*_/,">"new)) + 1' new="mydesired_name_" fasta_file

Resulting :
Code:
>mydesired_name_45
atatagcaga
>mydesired_name_46
atatagcagaatatatat

---------- Post updated at 08:44 AM ---------- Previous update was at 08:44 AM ----------

it worked nicely. Thank you
# 5  
Old 12-30-2013
Please use CODE TAGS for data you provided in post1. Select data and press code option which is available between QUOTE and HTML, I attached screen shot of it see.
Last edited by Akshay Hegde; 05-31-2014 at 04:29 PM..
# 6  
Old 12-30-2013
Hello,

One more approach with sed may help.

Code:
sed 's/\(^>.*_\)\(.*\)/my_desired_text_\2/g' file_name

Output will be as follows.

Code:
my_desired_text_45
atatagcaga
my_desired_text_46
atatagcagaatatatat



Thanks,
R. Singh

---------- Post updated at 11:34 AM ---------- Previous update was at 10:30 AM ----------

One more approach for same as follows.


Code:
awk -vs1="my_desired_ouput_" -F"_" '/^>/ {print s1$NF} !/^>/' file

Output will be as follows.

Code:
my_desired_ouput_45
atatagcaga
my_desired_ouput_46
atatagcagaatatatat


Thanks,
R. Singh
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