bioinformatics tools written in python for managing .fasta, .gff, BLAST results

FAshuff.py

Divide a genome in k-mers, shuffle and save the output.

python FAshuff.py -i genome.fasta -o shuffled.fasta -k 6

FAexclude.py

• -s --sequence
• -e --exclude
• -o --output

takes sequence and exclude exclude ids from the multifasta file. Saves the resulting .fasta in output

GFF3 files

Before using any gff parsing with pandas, headers should be removed.

cat ann.gff | sed '/^#/ d' > ann-clean.gff

now that pandas added the possibility to comment='#', this is not required anymore.

TODO more readme