Benson-Genomics-Lab / TRF

Tandem Repeats Finder: a program to analyze DNA sequences
https://tandem.bu.edu/trf/trf.html
GNU Affero General Public License v3.0
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Output machine-readable alignment #24

Open wiedenhoeft opened 7 months ago

wiedenhoeft commented 7 months ago

I would like to submit a feature request: So far, TRF outputs the query sequence to the .dat file or stdout. However, the alignment only appears in the HTML file. Parsing it out is possible, but error-prone.

Would it be possible to add two columns to the non-HTML output corresponding to the two alignment lines, with dashes (-) for indels and some separator (like | or ,) to demarkate the individual blocks that are separated by spaces in the HTML?