Augustus output, fasta with original contig name
0
0
Entering edit mode
2.9 years ago

Hello,

I need to predict genes in several thousand files and then analyses predicted proteins.

First, I have used Augustus and getAnnoFasta.pl to have a fasta file of proteins. The getAnnoFasta.pl give me a file with protein names like

>g1.t1 
>g2.t1
>g3.t1
..

But, I need to keep DNA contig names in my protein sequence names like

>dnacontig1.g1
>dnacontig1.g2
>dnacontig2.g1

or

>g1.dnacontig1
>g2.dnacontig1
>g1.dnacontig2

Don't matter the format, I just need to have the original contig name in the protein sequence name with the quickest method.

I think to used bedtools to extract my sequences in original files then translate sequences. Or, I think to make my homemade python script to extract sequences from Augustus outputs.

What is the best way? Thanks for your help.

gene • 712 views
ADD COMMENT
0
Entering edit mode

Hi, did you find the results, if yes kindly reply Thanks

ADD REPLY

Login before adding your answer.

Traffic: 2426 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6