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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
83 stars 17 forks source link

Provide results in a standard file format #33

Closed oschwengers closed 3 years ago

oschwengers commented 3 years ago

Hi @xiezhq , sorry for the flood of issues, but would also be possible to provide the final results (*.out) in a standardized file format like tsv?

For partial IS elements, the strand information is lacking which results in a row with 1 column less than for non-partial hits splitting the row at whitespaces like str.split() in python. By using tab as a separator, this would not be the case and it'd be much easier to automatically parse the results.

Best regards

xiezhq commented 3 years ago

Yes, I agree with you. Either .tsv or .csv will be better solution for the final result files output by ISEScan. I will implement this idea in the next version of ISEScan.

xiezhq commented 3 years ago

Update, the ISEScan v1.7.2.2 and later provide .csv (using , as column separator) and .tsv (using tab as column separator) files.

oschwengers commented 3 years ago

Thanks a lot for this update! I'm quite busy at the moment but I will definitely try this new release soon. I'll close this for now. Thanks