File format conversions

Renesh Bedre        1 minute read

File format conversions

  • bioinfokit will help you to convert the file formats for variety of tasks

Install bioinfokit

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

# 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)

How to cite?
Renesh Bedre.(2020, July 29). reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit (Version v0.9). Zenodo. http://doi.org/10.5281/zenodo.3965241

If you have any questions, comments or recommendations, please email me at reneshbe@gmail.com

Last updated: May 24, 2020

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.