Hi everyone,
I have a lot of .gff3 files with the CDS features and below with the fasta sequence. This sequence is separated from the CDS features like this:
##FASTA
>NZ_NZ_LR130533.1
I would like to extract all the fasta sequence into new fasta files, using as output for the fasta file the same name as the input gff3 file. I tried to use bedtools getfasta but that didn't work since I have multiple gff3 files for each input fasta.
Thanks in advance for your help!
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genomes_and_MGEs •
2 answers
Yes, each individual gff3 file has only a single fasta sequence at the end, right after the CDS features
Save this code in a file (file.py).
import sys
togg = False
ou =[]
fi = open(sys.argv[1])
ou = sys.argv[1].split('.')
w = open(ou[0]+".fa",'w')
for line in fi:
if ">" in line:
w.write(line)
togg = True
elif togg:
w.write(line)
else:
continue
fi.close()
w.close()
Run as follows:
python3 file.py my.gff
Result should be a my.fa with the sequence.
For multiple files at the same time:
for i in *.gff; do echo ${i}; python3 file.py ${i}; done
use sed to ignore everything befor the ##FASTA
zcat $gff | sed -n '/^##FASTA/,$p'
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Use
gffreadutility (LINK).Thanks for the answer, but if I understood correctly, this doesn't differ much from
bedtools getfastaand as so won't be of much help here. To explain better, I need to create a loop to extract only the fasta sequences inside the gff3 files, and output them into individual fasta files with the same name as the input gff3 files.Ah I see you have GFF3 files that have sequence in them (not common). Do you know if the sequence ends with a special block (like the
##FASTAbefore the start)?Exactly, it's not common. I just remembered I could use
bioawk -c fastx; if you have a better option, please let me know!If
bioawkworks then by all means. Otherwise this may need a small parsing program.can you post an example line or two?
There is no example needed.
GFF3 sequence sectionis described in specifications.genomes_and_MGEs : Do you have individual GFF files that contain just one entry/sequence?
Yes, each individual gff3 file has only a single fasta sequence at the end, right after the CDS features
Hi: To get protein fasta: cufflinks-2.2.1.Linux_x86_64/gffread genome.gff3 -g genome.fa -y genome_pro.fasta
To get cds fasta: cufflinks-2.2.1.Linux_x86_64/gffread genome.gff3 -g genome.fa -x genome_cds.fasta
This answer is not relevant so I will move it to a comment. OP has a unusual format GFF3 file that contains sequence inside it.