File format conversions
File format conversions
- bioinfokit will help you to convert the file formats for variety of tasks
Install bioinfokit
- Check bioinfokit documentation for installation and documentation
FASTQ to FASTA
Download test dataset
>>> from bioinfokit import analys
>>> analys.format.fqtofa(file="test_1.fastq")
# output will ve saved in same directory (output.fasta)
GFF3 to GTF
- Read detailed about GFF3 and GTF file formats
- Download dataset
# I am using interactive python interpreter (Python 3.8.2)
# supported in bioinfokit v0.8
>>> from bioinfokit.analys import gff
>>> gff.gff_to_gtf(file="Athaliana_167_TAIR10.gene_chr1.gff3")
# converted gtf file will be saved in same directory (Athaliana_167_TAIR10.gene_chr1.gtf)
HMM to CSV
Convert table output obtained from hmmscan (HMMER tool) to CSV format Download test dataset
>>> from bioinfokit import analys
>>> analys.format.hmmtocsv(file="test_hmm.txt")
# output will ve saved in same directory (output_hmm.csv)
TAB to CSV
Download test dataset
>>> from bioinfokit import analys
>>> analys.format.tabtocsv(file="test_tab.txt")
# output will ve saved in same directory (output.csv)
CSV to TAB
Download test dataset
>>> from bioinfokit import analys
>>> analys.format.csvtotab(file="test_csv.csv")
# output will ve saved in same directory (output.txt)
If you have any questions, comments or recommendations, please email me at reneshbe@gmail.com
This work is licensed under a Creative Commons Attribution 4.0 International License
