OboScanners for GeneOntology Files

September 14, 2007 (dg)

Mode/Lines	1	10	100	1000	10000	100000	250000	Memory (Mb)
flex	0.001	0.001	0.001	0.004	0.015	0.182	0.313	2.13
java15	0.132	0.135	0.132	0.242	0.623	1.273	2.130	79
java15_x64	0.137	0.133	0.133	0.233	0.581	1.240	2.288	ND
java16	0.131	0.134	0.131	0.205	0.441	1.194	1.963	800
perl	0.031	0.031	0.031	0.032	0.066	0.384	0.961	7
plex2.0_32	0.001	0.001	0.002	0.011	0.109	1.011	2.765	0.8
plex2.2_32	0.001	0.001	0.003	0.012	0.123	1.136	3.136	1
plex2.2_64	0.002	0.001	0.003	0.016	0.155	1.479	3.808	1
tcl	0.090	0.089	0.092	0.123	0.439	3.392	8.724	6

Java-Memory Observations

September 13, 2007 (dg)

A problem with Java based applications is the hugh memory amount required to run the scanner. Tested were diffeent settings of the maximum memory allocation pool using the commandline option -Xmx.

Mode	1	10	100	1000	10000	Memory (Mb)
java	0.14	0.256	0.453	1.708	15.500	788
java -Xmx16m	0.174	0.260	0.436	1.728	15.598	290
java -Xmx32m	0.175	0.255	0.457	1.713	15.576	308
java -Xmx64m	0.175	0.254	0.456	1.713	15.460	339
java -Xmx128m	0.156	0.255	0.441	1.708	15.607	404
java -Xmx256	0.156	0.253	0.421	1.714	15.520	532
java -Xmx512	0.155	0.253	0.456	1.709	15.507	795

OboScanner

September 13, 2007 (dg)

Comparing 64 and 32bit Scanners generated with the tply-lexer for pascal (free pascal) and with the jflex-Lexer for Java. Java programs require about 800Mb of memory whereas the pascal programs require just 1Mb of memory. However the Java programs where faster with the complete gene ontology obofile (about 250000 lines).

Mode/Lines	1	10	100	1000	10000	100000	250000
obo-plex32	0.001	0.001	0.003	0.015	0.142	1.334	3.623
obo-plex64	0.001	0.001	0.003	0.015	0.160	1.448	4.038
obo-java15_x64	0.140	0.135	0.133	0.206	0.623	1.297	2.241
obo-java15	0.133	0.136	0.137	0.208	0.596	1.352	2.028
obo-java16	0.134	0.132	0.134	0.215	0.465	1.117	1.943

WC-Comparisons

September 12, 2007 (dg)

Again the same set of blastfiles was used for testing of a word counting scanner. Flex and re2c based scanners again were performing best.

Mode	1	10	100	1000	10000
wc-flex	0.003	0.011	0.102	1.083	12.459
wc-flexpp	0.026	0.169	1.940	21.193	244.294
wc-gcj-exe	0.097	0.123	0.441	3.934	42.928
wc-gcj	0.087	0.307	2.875	30.163	nd
wc-java14	0.153	0.259	0.481	1.748	15.965
wc-java	0.176	0.257	0.444	1.704	15.682
wc-javaip14	0.122	0.345	2.774	28.982	329.265
wc-javaip	0.120	0.345	2.771	28.769	335.123
wc-perl-hand	0.006	0.018	0.155	1.590	18.132
wc-perl-lex	0.164	0.872	9.108	97.561	nd
wc-plex64	0.008	0.044	0.476	5.106	58.264
wc-plex	0.006	0.043	0.433	4.589	55.773
wc-re2c	0.002	0.005	0.035	0.346	3.975
wc-tcl8532	0.257	1.625	17.440	190.076	nd
wc-tcl8564	0.183	1.071	11.550	126.854	nd
wc-tcl	0.401	2.327	25.212	274.777	nd
wc-unix	0.006	0.026	0.285	2.937	33.792

BlastParsers vs BlastScanners

June 26, 2007 (dg)

We recently compared our newly generated Blast scanners with currently available BLAST-scanners from the BioJava-project (1), the BioPerl-project [2] and with the Zerg-BLAST parser [3]. Those parsers were compared with our scanners created either with C-based scanner generators like Re2c [4] and Flex [5] or with the Java based scanner generator Jflex [6]. Wheras the parsers mentioned above requires source code editing for parsing and analysing blast files our scanners are emitting SQL-code. Analyzing of blast results can afterwards done with a high level language (SQL). Please note that the BioJava scanner does not work with actual BLAST-versions. File sizes for the blast files has been about 1 (small), 14 (medium) and 140 (large) Mb

Mode	small	medium	large	memory(Mb)
blast-biojava	2.019	8.055	err	1054
blast-bioperl	4.026	47.822	nd	21
blast-flex	0.051	0.567	4.237	20
blast-jflex	0.607	1.906	8.532	863
blast-re2c	0.027	0.283	2.094	19.7
blast-zerg	0.017	0.185	1.331	6.5
blast-tclkit851	35.480	nd	nd	10.1

Comparison of several scanner generators for a simple BLAST scanner

April 10, 2007 (dg)

Sample: BlastFile with 1 to 10.000 result items

Mode	1	10	100	1000	10000
flex	0.003	0.015	0.199	1.979	25.548
flex-tcl	0.005	0.018	0.167	1.775	20.701
gcj	0.099	0.149	0.784	7.536	83.421
gij	0.109	0.482	4.917	51.939	nd
java	0.228	0.348	0.753	3.048	27.806
javaip	0.180	0.517	4.715	49.852	nd
plex	0.011	0.082	0.856	9.565	107.987
perl	0.031	0.050	0.235	2.280	23.916
re2c	0.004	0.012	0.076	0.765	8.438
tcl	1.702	12.524	140.249	nd	nd

The Re2c based scanner is the fastest, but the setup and the coding is more complicated than for the other scanners. Flex-based scanners are 2-3 times slower than Re2c based scanners, regardless if there is an embedded Tcl-interpreter for better string handling (flex-tcl), Jflex code (java), executed with the Sun-Java Hotspot virtual machine (1.5) as well as to machine code compiled Jflex code (java-gcj) and Plex (sbs-plex = Pascal lex) based scanners are about 5 and 10 times slower than Re2c based scanners. Interpreted Java-Code either executed with the Sun-interpreter (java-ip = “java -Xint”) or with the gnu-interpreter (java-gij) is about 50 times slower than Re2c-Code. The Tcl based scanner is about 1000 times slower than the Re2c based. The per scanner is a line based scanner thereof not able to do complicated scanning with more than two states or patterns on the same line.

Initial Setup of the Bioscanners and Bioparsers Webpage

March 13, 2007 (dg)

Project Aim

Write parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). These scanner generators are providing easier maintainance, development and higher speed than hand written scanners.