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 regex-dna benchmark hypotheses non fingo

↓ Match DNA 8-mers and substitute nucleotides for IUB codes, ~5MB N=500,000.

Which programs used least Code? Which programs use highly optimised assembly code libraries? Which programs make use of all the processor cores?

		sort	sort	sort	sort
×	Program & Logs	CPU secs	Elapsed secs	Memory KB	Code B	~ CPU Load
1.0	Tcl #2	3.30		25,004	373
1.7	OCaml #2	5.54		45,364	615
1.7	C++ GNU g++ #3	5.58		12,704	1588
1.8	C Intel #2	5.93		13,088	1099
1.8	Python CPython	6.04		20,516	342
1.8	C GNU gcc #2	6.09		13,360	1099
1.9	Pike #2	6.32		12,792	472
1.9	Python Psyco	6.43		19,576	355
2.0	BASIC FreeBASIC	6.48		99,864	1106
2.0	Lisaac	6.55		26,132	1299
2.2	C++ GNU g++ #2	7.24		19,832	635
2.3	D Digital Mars #2	7.54		86,596	506
2.3	Java 6 -Xms64m #4	7.60		75,192	921
2.4	Java 6 -server #4	7.81		75,892	921
2.5	Python IronPython #2	8.32		156,072	314
2.8	PHP #2	9.20		106,752	675
2.8	Scheme PLT	9.35		119,724	835
2.8	Ruby MRI	9.37		81,148	323
3.1	CAL	10.33		98,312	1334
3.2	Ruby 1.9	10.43		31,844	323
3.2	Scheme PLT #2	10.59		123,968	669
3.3	Java 6 -client #4	10.86		69,644	921
3.3	Nice #2	10.87		94,196	637
3.3	Lisp SBCL	10.88		276,452	586
3.6	Java 1.4 -server	11.79		73,376	657
3.6	Perl #4	11.81		21,408	431
3.8	Scala	12.41		92,956	663
4.2	Perl #2	13.71		24,852	449
4.3	Ada 2005 GNAT #4	14.08		14,496	1352
5.2	JavaScript SpiderMonkey	17.16		180,280	365
5.8	Forth bigForth #2	19.01		54,800	762
6.9	Groovy	22.73		112,176	366
7.3	Eiffel SmartEiffel	24.07		25,576	767
7.6	C# Mono #3	25.11		124,284	607
7.7	Python IronPython	25.29		170,448	342
7.7	C# Mono	25.41		157,420	624
8.3	Ruby JRuby	27.52		186,520	323
17	Ada 2005 GNAT #3	54.54		42,444	1233
20	Erlang HiPE #3	66.08		116,636	687
20	Smalltalk VisualWorks	66.74		44,092	584
39	Java 6 -Xint #4	130.26		66,972	921
115	Java GNU gcj	6 min		261,312	657
	C CINT	Failed			1101
	C++ Intel #2	Failed			635
	C++ Intel #3	Failed			1588
	D Digital Mars #3	Failed			1022
	JavaScript Rhino	Failed			592
	Mozart/Oz #2	Timed Out			589
	Pike	Timed Out			892
	Scheme Chicken	Failed			961
	Smalltalk GNU	Failed			502
interesting alternative programs
	Pascal Free Pascal #2	Failed			1074
	Fortran G95	Failed			2425
0.3	Pascal Free Pascal #3	1.10	0.00	19,604	2932
0.4	Perl #6	1.23	0.00	22,120	471
0.4	Perl #3	1.26	0.00	31,584	440
0.6	Icon #2	1.95	0.00	51,244	770
0.7	Perl #5	2.36	0.00	24,760	479
0.9	Python CPython #2	2.88	0.00	23,000	314
1.0	Perl	3.34	0.00	21,956	426
1.3	Fortran Intel	4.18	0.00	13,996	2425
1.3	Pascal Free Pascal	4.37	0.00	11,436	1199
1.4	CAL #2	4.67	0.00	67,648	1471
2.0	D Digital Mars #4	6.62	0.00	71,692	488
2.3	Ruby MRI #2	7.62	0.00	42,824	396
2.4	Lua LuaJIT #3	7.88	0.00	34,368	427
3.0	Lua #3	9.89	0.00	32,908	427
5.2	C# Mono #4	17.31	0.00	64,708	657
missing programs
	Clean	No program
	F# Mono	No program
	Forth GNU GForth	No program
	Fortran G95	No program
	Fortran Intel	No program
	Haskell GHC	No program
	Icon	No program
	Io	No program
	Lua	No program
	Lua LuaJIT	No program
	Mercury	No program
	Oberon-2 OO2C	No program
	Pascal Free Pascal	No program
	Prolog SWI	No program
	Prolog YAP	No program
	Rebol	No program
	Scheme Ikarus	No program
	Smalltalk Squeak	No program
	SML MLton	No program
	SML SML/NJ	No program
	Zonnon Mono	No program

 regex-dna benchmark : Match DNA 8-mers and substitute nucleotides for IUB codes

diff program output for this 100KB input file (generated with the fasta program N = 10000) with this output file to check your program is correct before contributing.

We use FASTA files generated by the fasta benchmark as input for this benchmark. Note: the file may include both lowercase and uppercase codes.

Each program should

• read all of a redirected FASTA format file from stdin, and record the sequence length
• use the same simple regex pattern match-replace to remove FASTA sequence descriptions and all linefeed characters, and record the sequence length
• use the same simple regex patterns, representing DNA 8-mers and their reverse complement (with a wildcard in one position), and (one pattern at a time) count matches in the redirected file
• write the regex pattern and count
• use the same simple regex patterns to make IUB code alternatives explicit, and (one pattern at a time) match-replace the pattern in the redirect file, and record the sequence length
• write the 3 recorded sequence lengths