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jeffdaily / parasail-python

Python bindings for the parasail C library.
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Semi-global alignment results printing #37

Closed suzannejin closed 5 years ago

suzannejin commented 5 years ago

I want to do pairwise semi-global alignments of a set of proteins that I have, and I couldn't find the option for printing the results as following: 

Target:         81 EVAKDADLVIEAIPE--IFDLKKKVFSEIEQYCP     112
                   |*||***||*|**|*  **|***|***|*****|
Query:         170 EEAKNLGLVAEVFPQERFWDEVMKLAREVAELPP     203

Length: 34
Identity:        11/34 (32.4%)
Similarity:      32/34 (94.1%)
Gaps:             2/34 ( 5.9%)
Score: 37
jeffdaily commented 5 years ago

You would like to fully duplicate the kind(s) of output from the parasail_aligner or the C API capabilities? I suppose I just assumed Python users would be my power users and not want output like this automatically.

Would you prefer that output like this be returned to you as a string? Or would you be okay with me simply exposing the C API that prints to C stdout?

suzannejin commented 5 years ago

Thanks for the answer. I've already managed to print the results as I wanted, although it could be great if it contains an option for printing or returning the stdout directly.