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Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Mon Jan 7 21:42:54 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
Update complete genome blast.

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Mon Jan 7 19:01:39 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.16: +85 -76 lines
Diff to previous 1.16
Fix variable scope issue. Put all excecutable content into a subroutine.

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Mon Jan 7 00:53:35 2013 UTC (6 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.15: +82 -132 lines
Diff to previous 1.15
Change blast against genomes to use the local SEED nr when available.
Switch to use BlastInterface.pm

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Tue Dec 20 01:45:48 2011 UTC (7 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.14: +46 -37 lines
Diff to previous 1.14
Fix the blast output similarity table.

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Fri Nov 11 00:23:10 2011 UTC (8 years ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_12152011, mgrast_release_3_1_2
Changes since 1.13: +58 -63 lines
Diff to previous 1.13
Some minor updates.

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Wed Sep 10 03:41:08 2008 UTC (11 years, 2 months ago) by golsen
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_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, 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, myrast_33, myrast_rel40, 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_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_release_2008_09_29
Changes since 1.12: +11 -4 lines
Diff to previous 1.12
Correct bug that caused failure to create the protein when it extended
beyond the visible windon.

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Sat Aug 23 23:39:22 2008 UTC (11 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.11: +11 -10 lines
Diff to previous 1.11
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Mon Jul 24 19:23:32 2006 UTC (13 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, 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
Changes since 1.10: +7 -5 lines
Diff to previous 1.10
Fix endpoint error when negative strand region runs off the start of the
contig.

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Fri May 5 14:38:00 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +2 -2 lines
Diff to previous 1.9
added new logging

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Thu Mar 2 22:32:42 2006 UTC (13 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.8: +9 -6 lines
Diff to previous 1.8
Don't report blast hits to deleted proteins.

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Thu Jan 19 19:03:39 2006 UTC (13 years, 9 months ago) by golsen
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.7: +118 -45 lines
Diff to previous 1.7
Fix the endpont of new coding sequences to include the stop codon (when
possible).

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Sat Jan 14 23:55:45 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.6: +84 -16 lines
Diff to previous 1.6
Fine tuning of the add a feature software.  (Still more to come in dealing
with previously deleted features)

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Thu Jan 12 05:18:59 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.5: +19 -17 lines
Diff to previous 1.5
Fix of the Shine-Dalgarno box location on the diagram.

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Thu Jan 12 04:14:24 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.4: +163 -18 lines
Diff to previous 1.4
Running version of adding a feature with a fid from the clearinghouse.

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Tue Jan 10 03:23:14 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.3: +437 -318 lines
Diff to previous 1.3
Many improvements.  This should now be fully functional, including allowing
the user to edit the genetic code and correctly spanning multile contig
segments (though there is no mechanism for the user to invoke this).

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Thu Jan 5 23:40:14 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.2: +202 -43 lines
Diff to previous 1.2
Improvements to the functionality including moving closer to being able
to create new features.  More diagnostics of state.  Some changes to the
way HTML is written (less use of the cgi package due to problems with
hidden inputs going way, or getting clobbered for mysterious reasons).
Add a map of other features in the displayed region.

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Wed Jan 4 23:49:59 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.1: +51 -37 lines
Diff to previous 1.1
Format the blast output table, link the blast matches to their SEED
entries, add organism names and do some other format clean-up.

Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Wed Jan 4 19:32:00 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
Add a page for proposing a new PEG.  This is not complete, and the 'create'
button is currently functionless, but it is worth some feedback as to the
direction it is headed.

The page is linked from the graphical display of tblastn output in index.cgi
(click on the "Q" object in the figure) (intentionally obscure for now).

Add a new blast output parsing perl package.  This can read from a file,
a pipe or a text array of lines (D=STDIN).  It can collect all output
(possibly memory intensive), or it can deliver quanta of output by being
called repeatedly with the same HANDLE or ARRAY (which can be made very
memory light).  It maintains separate state information for each input,
so multiple open streams works (silly me).  [Note that this is for full
text output, not the tabular output.  The alignments are also returned.
If you don't want them, slice-up the output with map{}.  You also get
useful information such as query and subject definitions (not just ids),
and their lengths.  There are huge quantities of description in the file.
It should work with all recent versions of blastall, and all -p options,
with the possible exception of tblastx, but it might work on that too.]
This package is intended to replace, and extend, all of the functionality
previously achieved by piping output through the rationalize_blast script.
Because it no longer requires the script, the shell invocation is no
longer required.  And this works with pipes opened with '-|', so ....
It is currently used in index.cgi and propose_new_peg.cgi.

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