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

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)

Please see this page to convert FASTQ to FASTA file format.

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

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