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Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 03:53:49 2011 UTC (9 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, myrast_33
Changes since 1.59: +49 -0 lines
Diff to previous 1.59 , to selected 1.28
Adjustments to loader utilities.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 6 20:01:39 2010 UTC (9 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.58: +0 -1 lines
Diff to previous 1.58 , to selected 1.28
Remove the "shebang".

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 22 20:40:18 2010 UTC (9 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.57: +4 -2 lines
Diff to previous 1.57 , to selected 1.28
Added support for Genetic Code 1.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 8 17:16:20 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.56: +37 -0 lines
Diff to previous 1.56 , to selected 1.28
Add SeedUtils::map_to_families for iterating over families.2c files.

Make filter_trunc_and_fs use that function, and have it delete singleton families.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 2 14:51:48 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.55: +9 -1 lines
Diff to previous 1.55 , to selected 1.28
add gunzip for fasta validate

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 6 17:11:47 2010 UTC (9 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.54: +33 -2 lines
Diff to previous 1.54 , to selected 1.28
Added quick hack to support function "genetic_code().

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 18 00:00:08 2010 UTC (9 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.53: +2 -0 lines
Diff to previous 1.53 , to selected 1.28
removing duplicate definition of AllColors

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 23:59:05 2010 UTC (9 years, 6 months ago) by redwards
Branch: MAIN
Changes since 1.52: +0 -2 lines
Diff to previous 1.52 , to selected 1.28
removing duplicate definition of AllColors

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 13 18:28:14 2010 UTC (9 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.51: +1 -1 lines
Diff to previous 1.51 , to selected 1.28
fix warning.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 21:16:10 2010 UTC (9 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.50: +1 -1 lines
Diff to previous 1.50 , to selected 1.28
better abbrev

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 21:10:17 2010 UTC (9 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.49: +5 -2 lines
Diff to previous 1.49 , to selected 1.28
better abbrev

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 19:24:25 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.48: +7 -0 lines
Diff to previous 1.48 , to selected 1.28
add strip_func_comment

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 23:17:17 2010 UTC (9 years, 7 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.47: +0 -2 lines
Diff to previous 1.47 , to selected 1.28
Removed calls to Tracer.pm routines.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 22 22:45:10 2010 UTC (9 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.46: +3 -0 lines
Diff to previous 1.46 , to selected 1.28
Fixed missing blank lines after '=cut' POD directives.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 22 22:37:27 2010 UTC (9 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.45: +127 -0 lines
Diff to previous 1.45 , to selected 1.28
Added useful functions 'file_read()' and 'file_head()'.

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:43:06 2010 UTC (9 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +1 -1 lines
Diff to previous 1.44 , to selected 1.28
removing dependencies

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 11 21:44:27 2010 UTC (9 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +108 -6 lines
Diff to previous 1.43 , to selected 1.28
fix abbrev

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 10 19:38:01 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.42: +142 -0 lines
Diff to previous 1.42 , to selected 1.28
Changes needed for DesktopRast.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 10 19:36:09 2010 UTC (9 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.41: +83 -0 lines
Diff to previous 1.41 , to selected 1.28
Add extract_seq from FIG.pm.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 30 19:04:13 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.40: +0 -1 lines
Diff to previous 1.40 , to selected 1.28
find_closest_genes support

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 22 12:20:06 2010 UTC (9 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +12 -0 lines
Diff to previous 1.39 , to selected 1.28
added run

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 21 15:59:36 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.38: +94 -1 lines
Diff to previous 1.38 , to selected 1.28
Add validate_fasta_file() that will scan a fasta for correctness, write
out a line-ending-corrected version, and return the type (dna or protein) of the
data in the file.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 20:21:50 2010 UTC (9 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.37: +62 -0 lines
Diff to previous 1.37 , to selected 1.28
Major update to figfams code. Remove old FigFam/FigFams modules that were tied to the
original decision procedure; update FF/FFs to use the Kmer-based stuff. Add new berkeley
db table processing routines to SeedUtils.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 9 20:14:26 2010 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.36: +50 -1 lines
Diff to previous 1.36 , to selected 1.28
Added "id_url" to compute URLs from gene IDs.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 29 20:33:43 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.35: +35 -0 lines
Diff to previous 1.35 , to selected 1.28
Updated per Gordon's email.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 12 01:06:54 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.34: +5 -0 lines
Diff to previous 1.34 , to selected 1.28
Changed boundaries_of to allow comma-delimited strings.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 25 16:10:54 2010 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.33: +57 -1 lines
Diff to previous 1.33 , to selected 1.28
BBH update

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 8 17:24:31 2010 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.32: +2 -1 lines
Diff to previous 1.32 , to selected 1.28
add the export

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 8 17:24:08 2010 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.31: +55 -0 lines
Diff to previous 1.31 , to selected 1.28
add verify_db

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 26 15:22:31 2010 UTC (10 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.30: +11 -6 lines
Diff to previous 1.30 , to selected 1.28
Fixed documentation for sims method.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 29 23:25:55 2010 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29 , to selected 1.28
Fixed the role-splitter.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 22 16:53:30 2010 UTC (10 years, 2 months ago) by dejongh
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.28: +0 -7 lines
Diff to previous 1.28
Removed extraneous curly bracket causing compilation error

Revision 1.28 - (view) (download) (as text) (annotate) - [selected]
Wed Jan 20 19:48:55 2010 UTC (10 years, 2 months ago) by disz
Branch: MAIN
Changes since 1.27: +14 -0 lines
Diff to previous 1.27
Added Strip_func

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 19 00:03:24 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26 , to selected 1.28
Fixed a comment.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 17 21:19:01 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.25: +1 -1 lines
Diff to previous 1.25 , to selected 1.28
Fixed error in the sims documentation.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 22:49:59 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24 , to selected 1.28
Minor bug fixes.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 21:17:49 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23 , to selected 1.28
Fixed an error in rev_comp.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 01:44:35 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.22: +14 -19 lines
Diff to previous 1.22 , to selected 1.28
New method for finding the ID of the protein sequence.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 15 17:44:42 2009 UTC (10 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.21: +28 -0 lines
Diff to previous 1.21 , to selected 1.28
add support for old SEED-format locations

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 22:22:28 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.20: +662 -701 lines
Diff to previous 1.20 , to selected 1.28
Minor fixes for Monday.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 02:11:58 2009 UTC (10 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +215 -0 lines
Diff to previous 1.19 , to selected 1.28
numerous changes

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 4 21:16:58 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.18: +154 -8 lines
Diff to previous 1.18 , to selected 1.28
Added location methods.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 3 15:34:16 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.17: +38 -3 lines
Diff to previous 1.17 , to selected 1.28
Added server to search for roles and/or functions in a genome.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 2 00:37:14 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.16: +36 -1 lines
Diff to previous 1.16 , to selected 1.28
Added method to parse roles from functional assignments.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 24 19:50:47 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.15: +46 -1 lines
Diff to previous 1.15 , to selected 1.28
Added method to parse a location string.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 24 19:23:36 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.14: +195 -6 lines
Diff to previous 1.14 , to selected 1.28
New methods for Sapling server.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 7 17:42:08 2009 UTC (10 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +46 -0 lines
Diff to previous 1.13 , to selected 1.28
added between

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 5 17:24:19 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.12: +71 -1 lines
Diff to previous 1.12 , to selected 1.28
Added "boundaries_of".

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 20 21:08:43 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.11: +4 -37 lines
Diff to previous 1.11 , to selected 1.28
Fixed to be SEED-independent.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 20 20:40:19 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.10: +65 -1 lines
Diff to previous 1.10 , to selected 1.28
Added a method to detect hypothetical assignments. Made a SAS component.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 11 19:53:27 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9 , to selected 1.28
Added a line feed at the end of FASTA strings.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 30 15:35:00 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.8: +69 -1 lines
Diff to previous 1.8 , to selected 1.28
Added a utility for parsing sequence input.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 2 20:28:21 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.7: +34 -1 lines
Diff to previous 1.7 , to selected 1.28
Added "verify_dir".

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 31 22:07:19 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.6: +31 -19 lines
Diff to previous 1.6 , to selected 1.28
Added stripped return format for "ids_to_fasta".

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 27 19:44:07 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.5: +199 -1 lines
Diff to previous 1.5 , to selected 1.28
Added a method for network sims retrieval.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 19 17:05:13 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.4: +63 -1 lines
Diff to previous 1.4 , to selected 1.28
Added "min" and "max" methods.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 3 21:31:42 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 , to selected 1.28
Updated to Sapling Server for Berkeley.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 23:37:46 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.2: +35 -1 lines
Diff to previous 1.2 , to selected 1.28
Updates for operon pipeline.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 20:11:54 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.1: +52 -1 lines
Diff to previous 1.1 , to selected 1.28
Additional functionality for sapling server.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 18 01:28:57 2009 UTC (10 years, 9 months ago) by parrello
Branch: MAIN
Diff to selected 1.28
New package for data-free utility methods.

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