Improvements to parse.py

[groutr]

Description of proposed changes

This PR implements some enhancements for parse.py. Some of the enhancements will improve performance by using common python idioms. Overall, memory used by parse.py should also be less since we don't read the entire fasta file into memory anymore.

Testing

The test suite passes. This PR fixes several suboptimal implementations of things with equivalent replacements as verified with manual testing.

The one place where I changed behavior is with prettify. It will now convert "Et Al." to "et al."

Thank you for contributing to Nextstrain!

[rneher]

Thanks @groutr! Sorry for the delay. this looks overall pretty good. But your implementation has one problem. It doesn't write out the sequences to file. By the time you arrive here:

augur/augur/parse.py

Line 119 in 693372a

SeqIO.write(seqs, args.output_sequences, 'fasta')

the iterator over the sequences is at the end and this writes an empty file. You either need to write these sequences to file as you loop over the input, or load them all into memory.

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[rneher]

thanks, this looks good. I'll test a few more use cases tomorrow.