Python reverse-complement Ruben Vorderman
Attach your source code file
Provide an example build command-line
python reverse_complement.py < fasta1000000001.txt > /dev/null
Performance
I am a bioinformatician. I program a lot in Python and this problem is right in my domain. So I thought I'd give it a shot.
Benchmarks performed using fasta1000000001.txt as highlighted in #520 (closed). Times measured by hyperfine. (cputime == usertime + systime). Memory usage measured using /usr/bin/time
| program | walltime (s) | cputime (s) | memory (MB) |
|---|---|---|---|
| This entry | 2.523 | 2.523 | 496 |
| #517 (closed) | 2.079 | 3.847 | 1467 |
| Python no6 | 3.986 | 5.902 | 2430 |
| Python no2 | 5.817 | 5.817 | 1750 |
Conclusion
Python can compete with the top-tier solutions on the memory usage front as long as the programming techniques are right. I hope to illustrate that with this entry. Also the cputime got quite a bit better, so this should push Python up quite a bit on the ranking page on both cputime and memory. It is quite a useful and fast scripting language when the proper techniques are used.
I added a huge swat of comments on the bottom of the entry to explain the techniques, for educational purposes.