by Daniel J leite
The script has been written for Python3.7.
It uses BioPython which can be install as shown here (https://biopython.org/wiki/Download).
The script was originally written to generate a GTF from transcriptomes that lack genomes assemblies. This was useful for creating necessary GTF files for transcriptomes during the cellranger mkref command for analysing 10x Genomics single cell RNAseq data.
This python3.7 script takes a fasta file and generates a GTF file. For each of the sequences present in the fasta file, three lines are generated in the GTF file, relating to gene, transcript and exon.
fasta2GTF.py only requires a fasta file as an input (-i) and the specified location of the output GTF (-o). The help option (-h) in the command line also shows these requirements.
Options:
-h help, display options
-i full path and name of input fasta file
-o full path and name of output GTF file
For example:
$ python3.7 fasta2GTF.py -i /path/to/fasta_input.fa -o /path/to/GTF_output.fa