Thanks for all those suggestions, I have implemented chop so far and got a solid 25% saving, even with overhead of reverse. Very worthwhile. Program run time is 5 minutes as one-off, 45 minutes in a full test suite, so 25% is good saving
The responders who mentioned I didn't give much context are of course correct, but I chose brevity. I have all sorts of requirements re scanning the protein strings, and I'm happy with my regexp scans, index's, other such things that use the structure of a ~20 character peptide sequence within the ~400 character protein, those are pretty ok and are not topping the list in the FastProf profile, just the areas where I do a dumb-as-hell one character at a time scan. These inlcude things like scanning all the proteins and looking for an essentially arbitrary logic in the strings, ie. break the protein (as per Trypsin protease) at a K or R, and count the S,T.Y residues in each segment. I don't think there's any way to speed that up with pre-processing and clever mapping and saving results for re-use, you just have to come up with the world's best way to scan down strings one char at a time. That's my take aayway.
I'll keep looking at your replies though, thanks again.
Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
Read Where should I post X? if you're not absolutely sure you're posting in the right place.
Please read these before you post! —
Posts may use any of the Perl Monks Approved HTML tags:
You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
- a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
Link using PerlMonks shortcuts! What shortcuts can I use for linking?
See Writeup Formatting Tips and other pages linked from there for more info.
| & || & |
| < || < |
| > || > |
| [ || [ |
| ] || ] ||