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Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 27 07:17:03 2015 UTC (4 years, 8 months ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD
Changes since 1.33: +10 -5 lines
Diff to previous 1.33
Fixed parsing failure in case when TAXONOMY string consists of a single field without semicolons.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 20:28:25 2011 UTC (8 years, 10 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.32: +42 -33 lines
Diff to previous 1.32
Added "-user_trans_only" flag.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 31 14:33:30 2010 UTC (9 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
Allow files with spaces in the name.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 10 20:05:39 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.30: +20 -2 lines
Diff to previous 1.30
Allow -i=input-file for specifying input, instead of stdin.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 10 19:35:36 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.29: +15 -11 lines
Diff to previous 1.29
Change to use SeedUtils instead of FIG.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 27 19:40:57 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.28: +4 -4 lines
Diff to previous 1.28
fixes for paths with spaces

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 12 17:32:59 2010 UTC (9 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.27: +7 -4 lines
Diff to previous 1.27
Fixed fact that we are still handling RNA functions as aliases, not functions.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 19 21:23:40 2010 UTC (9 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.26: +46 -30 lines
Diff to previous 1.26
Fixed mistrapping of "fuzzy" boundaries.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 11 22:42:51 2010 UTC (9 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.25: +45 -46 lines
Diff to previous 1.25
Fixed bug in code for missing translations.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 6 21:45:53 2010 UTC (9 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.24: +1 -0 lines
Diff to previous 1.24
Fixed "newline in /db_xref" bug.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 6 19:36:49 2009 UTC (10 years ago) by redwards
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
correcting ORIGIN regexp

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 26 20:34:07 2009 UTC (10 years, 7 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.22: +13 -12 lines
Diff to previous 1.22
Fixed parsing bug on optional arguments

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 05:49:34 2009 UTC (10 years, 8 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.21: +6 -1 lines
Diff to previous 1.21
Fixed spurious newlines in assigned functions and missing aliases; removed fatal abort if Genbank file does not contain any CDS entries.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 05:40:23 2009 UTC (10 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.20: +1 -1 lines
Diff to previous 1.20
Fixed spurious newlines in assigned functions and missing aliases; removed fatal abort if Genbank file does not contain any CDS entries.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 4 05:34:49 2009 UTC (10 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.19: +21 -16 lines
Diff to previous 1.19
Fixed spurious newlines in assigned functions and missing aliases; removed fatal abort if Genbank file does not contain any CDS entries.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 6 18:52:59 2009 UTC (10 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.18: +1 -1 lines
Diff to previous 1.18
bugfix

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 30 13:03:27 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.17: +314 -155 lines
Diff to previous 1.17
Cleaned up code; added "use strict" and "use warnings"; added annotations and EC_number extraction.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 14 15:56:47 2008 UTC (11 years, 6 months ago) by wilke
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_release_2008_09_29
Changes since 1.16: +21 -2 lines
Diff to previous 1.16
ids have prefixes now , e.g for locus tags locus|ID

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 11 04:27:40 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.15: +130 -174 lines
Diff to previous 1.15
Fixed ORIGIN parsing bug, blank line parsing bug. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 21:02:57 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +3 -0 lines
Diff to previous 1.14
fix parse_genbank to extract genome and taxonomy a bit more accurately

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 20:52:40 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +20 -3 lines
Diff to previous 1.13
fix parse_genbank to extract genome and taxonomy a bit more accurately

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 00:04:13 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +13 -16 lines
Diff to previous 1.12
Fixed bug parsing function. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.11: +17 -0 lines
Diff to previous 1.11
Add license words.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 2 14:54:34 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.10: +22 -8 lines
Diff to previous 1.10
Fixed bug in function-parsing logic. -- /gdp

Revision 1.9.2.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 27 15:26:44 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3
Changes since 1.9: +8 -6 lines
Diff to previous 1.9 , to next main 1.34
Merged from trunk.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 01:18:03 2005 UTC (14 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Changes since 1.9: +8 -6 lines
Diff to previous 1.9
Modified to not trim STOP off locus. -- /gdp

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 16 21:54:14 2004 UTC (15 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: Root-bobdev_news, efrank-preMakefileToStandardMk
Branch point for: Branch-bobdev_news
Changes since 1.8: +80 -25 lines
Diff to previous 1.8
Corrected bugs; added checks and debugging information for loci whose sequences could not be extracted.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 12 11:15:56 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +12 -5 lines
Diff to previous 1.7
update parse_genbank

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 5 19:55:34 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +4 -1 lines
Diff to previous 1.6
do not keep pseudo genes in parse_genbank

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 5 13:30:22 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fix serious bug causing truncation of CDSs in parse_genbank

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 3 21:03:42 2004 UTC (15 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
Fixed parsing error. -- /gdp

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 03:29:26 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +88 -20 lines
Diff to previous 1.3
allow complete option on genomes

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 9 19:18:21 2004 UTC (15 years, 10 months ago) by efrank
Branch: MAIN
Changes since 1.2: +12 -10 lines
Diff to previous 1.2
fix parse_genbank bugs

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 19:39:29 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.1: +86 -10 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01

Makefile:
	get it to work with the release tools

All the rest:
	had to rename foo to foo.pl so that makefiles could recognize
	perl source from, say, Makefiles and READMEs

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