[Bio] / FigKernelScripts / verify_genome_directory.pl Repository:
ViewVC logotype

Log of /FigKernelScripts/verify_genome_directory.pl

Parent Directory Parent Directory


Links to HEAD: (view) (download) (as text) (annotate)
Links to mgrast_dev_10262011: (view) (download) (as text) (annotate)
Sticky Tag:

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 7 18:49:34 2011 UTC (9 years 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_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.41: +1 -1 lines
Diff to previous 1.41
Added recognition of "contig.properties" file.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 21 20:44:11 2011 UTC (9 years ago) by redwards
Branch: MAIN
Changes since 1.40: +7 -0 lines
Diff to previous 1.40
checking for taxon id

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 28 16:04:27 2010 UTC (9 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119
Changes since 1.39: +74 -57 lines
Diff to previous 1.39
Made script more robust; suppressed some tests for "special_pegs" entires.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 16 17:56:08 2009 UTC (10 years, 10 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.38: +7 -5 lines
Diff to previous 1.38
Replaced all instances of `cat $file` and `head -1 $file` with &FIG::file_read($file) and &FIG::file_head($file, 1), respcectively.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 8 21:23:18 2008 UTC (11 years, 2 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.37: +36 -33 lines
Diff to previous 1.37
Hacks to make RNA-content checker non-fatal and less persnickety.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 2 12:46:18 2008 UTC (11 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.36: +26 -11 lines
Diff to previous 1.36
Allowed validity of AA-amibig "J", and corrected display of invalid AA-chars. Removed support for ambiguous "could-be-STOPs".

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 5 21:54:01 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, 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_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 1.35: +100 -0 lines
Diff to previous 1.35
Augmented genetic code table to translate ambiguous codons that _could_ be STOPs as being valid STOPs. -- /gdp

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 6 17:53:33 2008 UTC (11 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.34: +30 -13 lines
Diff to previous 1.34
Hack adding switch to suppress fatality of non-STOP terminated PEGs. Proper rewrite under development.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 12 21:06:13 2008 UTC (11 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
Don't consider contigs.btree when looking for contigs.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 19 03:09:01 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.32: +4 -2 lines
Diff to previous 1.32
Modified to accept lower-case "x" in a protein sequence. -- /gdp

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 10 20:44:18 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
Fixed obsolete reference to $_. -- /gdp

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 22:36:16 2007 UTC (12 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.30: +1 -1 lines
Diff to previous 1.30
Suprress announcement of genetic code unless VERBOSE is set. -- /gdp

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 19:00:23 2007 UTC (12 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.29: +152 -214 lines
Diff to previous 1.29
Added alternate genetic code support. -- /gdp

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 17:03:29 2007 UTC (12 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
Modified to reflect changes in BLAST DB names. -- /gdp

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 22 22:36:07 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +7 -0 lines
Diff to previous 1.27
Added check for untranslated PEGs. -- /gdp

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 21 15:53:30 2006 UTC (13 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
fixes to split_and_trim

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 18:56:38 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.25: +17 -0 lines
Diff to previous 1.25
Add license words.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 22 14:57:50 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
fixes to characterization of hypos

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 2 14:52:49 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
Minor change in diagnostic statement. -- gdp

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 30 19:23:52 2005 UTC (14 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.22: +5 -1 lines
Diff to previous 1.22
	    # the DB_File below changes an 11' run into 19', so i've upped the
	                # threshold to 20GB to turn this off for now until a better
				    # fix is done (read tbls first and hash it rather than contigs)

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 30 17:35:01 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +23 -0 lines
Diff to previous 1.21
Total up contig size, and if >2G, tie %seqs_of to a DB_File hash.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 13 13:34:50 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +25 -9 lines
Diff to previous 1.20
fixes to computing starts

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 31 21:12:59 2005 UTC (14 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +62 -22 lines
Diff to previous 1.19
Added checks for Taxon-ID and sequence content. -- /gdp

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 14 21:32:48 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.18: +53 -0 lines
Diff to previous 1.18
Add some checks on assignments file.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 15 15:40:13 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news, 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 1.17: +4 -0 lines
Diff to previous 1.17
Added diagnosits for bad STOPs. (Need to add "truncated PEG" logic.) -- /gdp

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 30 05:20:14 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: efrank-preMakefileToStandardMk
Changes since 1.16: +6 -5 lines
Diff to previous 1.16
Added printout of record-number to diagnostic msgs. -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 17 20:00:37 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +70 -2 lines
Diff to previous 1.15
fixes to extract_genomes

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 11 16:18:58 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +79 -44 lines
Diff to previous 1.14
Added checks for dupicated FIDs. -- /gdp

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 19:24:39 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.13: +6 -1 lines
Diff to previous 1.13
Fixed bug that script falsely exits with an "O.K." condition when GENOME, PROJECT or TAXONOMY files are missing. -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 4 19:47:24 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +18 -4 lines
Diff to previous 1.12
add some files to extracted Global

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 24 17:36:02 2004 UTC (15 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
Allow Data directory as input to build_nr_sources

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 20 16:04:15 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Fixed wart locating 'contigs' files. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 1 19:48:37 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
minor fixes to exporting sets

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 15:22:22 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +37 -28 lines
Diff to previous 1.8
Added check for bad chars in contigs; made output more informative. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 2 21:50:54 2004 UTC (15 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.7: +32 -25 lines
Diff to previous 1.7
Fixed bug in RNA section; minor cosmetic changes.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 2 15:05:53 2004 UTC (15 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.6: +19 -11 lines
Diff to previous 1.6
Modified code so that error go to STDOUT and warnings go to STDERR

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 18 22:21:10 2004 UTC (15 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.5: +20 -3 lines
Diff to previous 1.5
Added heuristic check for duplicate contig sequences.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 16 16:28:58 2004 UTC (15 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.4: +9 -1 lines
Diff to previous 1.4
Added check for duplicate contig-IDs.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 29 18:59:17 2004 UTC (15 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.3: +33 -15 lines
Diff to previous 1.3
Added code to check PEG fasta files for invalid chars.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 21 20:05:45 2004 UTC (15 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.2: +9 -6 lines
Diff to previous 1.2
Added numerous checks of genome directory-structure

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 16:36:04 2004 UTC (15 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.1: +216 -11 lines
Diff to previous 1.1
Added numerous consistency checks

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (16 years, 2 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01, delong-01, delong-02

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

This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, select a symbolic revision name using the selection box, or choose 'Use Text Field' and enter a numeric revision.

  Diffs between and
  Type of Diff should be a

Sort log by:

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3