Convert MitoAnnotator (MitoFish) annotation file to NCBI feature table format (*.tbl)
The script mitofish2tbl.py was developed and tested with Python 2.7.12 and is part of the supplementary material of the article Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.) by Steven J. Weiss, et al. 2020. Organisms Diversity and Evolution. doi: 10.1007/s13127-020-00468-7
The directory testdata contains annotation results obtained from the Mitofish annotation pipeline (link, last accessed 26.11.2020). The original DNA sequence submitted is in the file testdata/Thy10.fa.
The script takes exactly one input file (mitoannotator annotation file, e.g. annotation.txt) and produces one output file (annotation in tbl format, e.g. annotation.tbl). Per default the output file will have the same prefix as the input txt file and will be written to the same location as the input file.
Try it, like so:
(host)-$ ./mitofish2tbl.py testdata/Thy10.txt
mitofish file to convert: testdata/Thy10.txt
writing to: testdata/Thy10.tbl