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Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 14 17:26:09 2008 UTC (11 years ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD, 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_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.8: +1 -2 lines
Diff to previous 1.8
Fixed leading-whitspace bug.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 13 01:33:23 2006 UTC (13 years, 7 months ago) by overbeek
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_04_23, 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_release_2008_09_29
Changes since 1.7: +33 -8 lines
Diff to previous 1.7
leave master: on subsystem_curator

Revision 1.7 - (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 1.6: +17 -0 lines
Diff to previous 1.6
Add license words.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 21 19:52:32 2005 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +10 -5 lines
Diff to previous 1.5
Modified to accept skeleton OrgDirs as arguments, not just installed OrgIDs. -- /gdp

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 16 22:36:49 2005 UTC (14 years, 2 months ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.4: +13 -2 lines
Diff to previous 1.4
assess_completeness required the organism to be loaded in seed in order
to run becaus it used FIG::is_eukaryotic and is_prokaryote.  However,
assess_completeness is *called* from add_genome during the load of a
new org and in that circumstance, it must fail.

Since TAXONOMY file is in the directory being loaded, just read it
directly in assess_completeness and test ourselves.

add_genome now correctly reports completeness (only tested on c elegans
though).

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 13 13:34:50 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +2 -0 lines
Diff to previous 1.3
fixes to computing starts

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 4 21:13:08 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news, efrank-preMakefileToStandardMk, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Changes since 1.2: +22 -10 lines
Diff to previous 1.2
fixes to start predictions

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 18:05:28 2005 UTC (14 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +2 -2 lines
Diff to previous 1.1
fix to asses_completeness

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 23:42:09 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
assess_completeness reads the contigs in one or more specified genome
directories and either writes or erases a file called PROBABLYCOMPLETE
depending on whether > 70% of the nucleotides are in contigs > 20 kbp.
Both of these parameters can be set with command line options.

fastasize is used by assess_completeness to determine the lengths of
the contigs in the files.

I still need to find the makefile changes (if any) so that fastasize
gets compiled and installed.

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