Question: genome features and sequence parsing
0
gravatar for lessismore
2.3 years ago by
lessismore670
Mexico
lessismore670 wrote:

Hello people, need to parse the cds fraction of a genome based on a gff3 file and a genome file. Do you know any good parser for that? For the moment i am with:

cat mygenome.gff3 | awk -v FS="\t" -v OFS="\t" '$3 == "CDS" {print $1, $4-1 ,$5, $1":"$4"-"$5":"$9}' | bedtools getfasta -name -fi mygenome.fasta -bed - -fo cds.fa

please note: in this annotation exons are identified as cds1/cds2/cds3 etc..

At this point i just got all cds for each transcript. But my aim is: for each transcript parse the complete CDS sequence after joining all the cds1 cds2 cds3 etc.. also based on strand orientation.

In summary i want a table like this: chrom | coord. cds | seq (CDS)

do you have any clues for me? thanks

parsing sequence cds genome • 661 views
ADD COMMENTlink modified 2.3 years ago by Macspider2.9k • written 2.3 years ago by lessismore670
1

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k

thanks, can you also tell me how you printed the pic of this page that you just posted?

ADD REPLYlink written 2.3 years ago by lessismore670
1

Directly next to the button for code markup is a button for inserting images. You need to put the picture online somewhere, I use tinypic but there are many alternatives.

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k
0
gravatar for Macspider
2.3 years ago by
Macspider2.9k
Vienna - BOKU
Macspider2.9k wrote:

You're looking for getAnnoFasta.pl from the Augustus programs:

http://bioinf.uni-greifswald.de/augustus/binaries/scripts/getAnnoFasta.pl

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Macspider2.9k
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