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Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 3 05:35:03 2009 UTC (10 years, 7 months ago) by redwards
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_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 1.28: +2 -2 lines
Diff to previous 1.28
removing check for refseq ids

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 5 20:49:50 2007 UTC (12 years, 9 months ago) by redwards
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_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_release_2008_09_29
Changes since 1.27: +12 -0 lines
Diff to previous 1.27
Just adding comments and docs

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 26 19:38:00 2006 UTC (13 years, 2 months ago) by redwards
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
correctingoutput comment

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 24 15:04:38 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +2 -2 lines
Diff to previous 1.25
Fixed typos in usgae msg. -- /gdp

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 11 11:15:44 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +46 -14 lines
Diff to previous 1.24
Added check against clobbering existing FIDs during append. -- /gdp

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 4 15:38:55 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +5 -1 lines
Diff to previous 1.23
RAE: Fixing translation bug in gff2seed

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 4 05:32:50 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
RAE: Adding FigKernelScripts/extract_fasta_idmap.pl

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 5 00:45:20 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.21: +60 -9 lines
Diff to previous 1.21
RAE: Updating GFF files for extracting data from TIGR

Revision 1.21 - (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
Changes since 1.20: +17 -0 lines
Diff to previous 1.20
Add license words.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 20:57:51 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
;
:wq

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 19:04:06 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.18: +13 -2 lines
Diff to previous 1.18
gff2seed:	use description, Note, and nci_annotation in that order to define
		annotatioin and assignment.  ncbi is source for the final case.
		otherwise, set to gff2seed

embl2gff:	include unigene, EMBL: and protein_id. include assignment from
		parse_mart (below) into Note attribute in gff

parse_mart:	pull in assignemtn from transcript feature file.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 5 21:38:21 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
embl2gff- add ensembl protein id
gff2seed- sort the fetaures before writing to tbl file.
parse_mart- rename ChromBand to just Band

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 29 21:46:06 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.16: +9 -13 lines
Diff to previous 1.16
Ensure no duplicates are put in the peg aliases in the tbl file.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 29 00:20:03 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
gff2seed:  fix typo in arg processing that made -append be ignred.

embl2gff: pass in org version number, extras file name

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 28 18:06:18 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.14: +35 -2 lines
Diff to previous 1.14
Create annotations and assigned_function files based on the ncbi_annotation attribute, if present.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 28 17:02:34 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.13: +87 -25 lines
Diff to previous 1.13
More gff2seed mods. Support translation of dbxrefs to seed aliases.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 27 21:21:50 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.12: +76 -27 lines
Diff to previous 1.12
Modify to allow multiple gff files to be gathered into a single directory.
Added the command option, -append.

If you do not have -append and the directory already exists in tmp, it is an error
just as before.

If you do have -append and the directory does NOT exist already, it is an error as
you must run first without append.

When you run -append and when there's already an unacked directory in tmp, the
behavor of gff2seed is:
   1. for the base files like TAXONOMY etc., just leave them alone.  Assume the
      first run got it right.
   2. for everything but the contigs file, append to the existing files.
   3. For the contigs file, look for files of the form contigs\d*.  Find
      the biggest value of (\d*), bump it up by one, and put the contigs there.

The idea is to run gff2seed as many times as needed to gather the gff's into
the unpacking directory, then run fig load_genome *exactly* once, just as
before.

This is all needed to avoid making huge contigs files and huge gff files
for big orgs (euks).

CAVVEAT:  i think the fasta files are ok, but will have to come back and revist
that if they are too big like the contigs.

How's that for a commit message.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 27 19:12:10 2005 UTC (14 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.11: +10 -0 lines
Diff to previous 1.11
Fix a bug that cause small gffs to load incorrectly.


# the size test below returns zero for small files so force a
# flush.  I'm not sure if this is as robust as doing autoflush()
# from the start, but that seems unduly expensive until proven
# a problem.

$pegfeatfh->flush();
$pegseqfh->flush();
$rnafeatfh->flush();
$rnaseqfh->flush();

for my $what ('peg', 'rna')
{

my $size=-s "$genomedir/Features/$what/fasta";
    if (-s "$genomedir/Features/$what/fasta" == 0 and -s "$genomedir/Features/$what/tbl" == 0)

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 16 15:35:33 2005 UTC (14 years, 3 months ago) by redwards
Branch: MAIN
Changes since 1.10: +9 -4 lines
Diff to previous 1.10
Updating seed2gff and gff2seed for round-robins

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 20:07:41 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +1 -2 lines
Diff to previous 1.9
debugging and highlighting

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 15:23:00 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -3 lines
Diff to previous 1.8
stop icrememnting genome number

Revision 1.5.2.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 15:39:01 2005 UTC (14 years, 4 months ago) by olson
Branch: Branch-bobdev_news
CVS Tags: merge-bodev_news-3
Changes since 1.5.2.1: +9 -3 lines
Diff to previous 1.5.2.1 , to branch point 1.5 , to next main 1.29
Merged changes from trunk.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 14:36:14 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
CVS Tags: merge-trunktag-bodev_news-3
Changes since 1.7: +0 -2 lines
Diff to previous 1.7
unbreaking gff2seed.pl

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 11 21:25:03 2005 UTC (14 years, 4 months ago) by redwards
Branch: MAIN
Changes since 1.6: +11 -3 lines
Diff to previous 1.6
changing raedraw and raelib

Revision 1.5.2.1 - (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
Changes since 1.5: +133 -111 lines
Diff to previous 1.5
Merged from trunk.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 22 20:09:41 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2
Changes since 1.5: +133 -111 lines
Diff to previous 1.5
Remove Features/xxx dir when xxx has no features.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 24 16:33:26 2005 UTC (14 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.4: +2 -3 lines
Diff to previous 1.4
minor changes to gff2seed/FigGFF

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 10 00:15:17 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
CVS Tags: efrank-preMakefileToStandardMk
Changes since 1.3: +1 -1 lines
Diff to previous 1.3
addition to gff2seed

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 9 23:42:32 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.2: +17 -4 lines
Diff to previous 1.2
gff2seed directory passes all checks

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 9 21:09:30 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
Changes since 1.1: +2 -5 lines
Diff to previous 1.1
minor changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 9 21:04:48 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
initial commit of gff2seed to go from gff3 to seed directory

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