How to extract sequence of a specific feature in gff

Question

[tianshenbio]

I have a gff file like this:

Bany_Scaf24 maker   gene    41357   46444   .   +   .   ID=Bany_09696;Name=Bany_09696;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0;
Bany_Scaf24 maker   mRNA    41357   46444   .   +   .   ID=Bany_09696-RA;Parent=Bany_09696;Name=Bany_09696-RA;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=277|1|1|1|0|0|2|35|76;_eAED=0.00;score=1829;
Bany_Scaf24 maker   exon    46189   46444   .   +   .   ID=Bany_09696-RA:1;Parent=Bany_09696-RA;
Bany_Scaf24 maker   exon    41357   41643   .   +   .   ID=Bany_09696-RA:2;Parent=Bany_09696-RA;
Bany_Scaf24 maker   five_prime_UTR  41357   41633   .   +   .   ID=Bany_09696-RA:five_prime_utr;Parent=Bany_09696-RA;
Bany_Scaf24 maker   CDS 41634   41643   .   +   0   ID=Bany_09696-RA:cds;Parent=Bany_09696-RA;
Bany_Scaf24 maker   CDS 46189   46409   .   +   2   ID=Bany_09696-RA:cds;Parent=Bany_09696-RA;
Bany_Scaf24 maker   three_prime_UTR 46410   46444   .   +   .   ID=Bany_09696-RA:three_prime_utr;Parent=Bany_09696-RA;
B

I also have the genome fasta file. How do I generate two fasta files of 'gene' and 'three_prime_UTR' based on the the coordinates?

[lieven.sterck]

have you looked into this toolbox: https://github.com/NBISweden/AGAT , likely it will hold some function that does this.

[GenoMax]

You should search Biostars for questions such as these since this has been asked and answered before. Use google (or your fav search engine) to search externally.

How to extract exon sequences from annotated genome
Extracting transcript sequences with gene name (gffread)
http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread

Answer 1

[Juke34]

Yes you can definitely do it with agat_sp_extract_sequences.pl from AGAT
e.g for three_prime_UTR feature:
agat_sp_extract_sequences.pl --gff input.gff --fasta input.fasta -t three_prime_UTR