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Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 18 19:43:04 2010 UTC (9 years, 3 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_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_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.7: +2 -2 lines
Diff to previous 1.7
Fix two minor typographical errors in the documentation.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 18 19:32:15 2009 UTC (9 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.6: +3 -0 lines
Diff to previous 1.6
add as SAS components

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 11 15:11:27 2009 UTC (10 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.5: +15 -13 lines
Diff to previous 1.5
Fix to bug that caused failure in reading alignments with an entire row
of gaps.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 1 21:06:10 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix unitialized variable

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:50:43 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +49 -7 lines
Diff to previous 1.3
fixes to support search for rRNAs

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 25 18:14:45 2008 UTC (11 years ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05
Changes since 1.2: +2 -0 lines
Diff to previous 1.2
updates from Gary

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 2 22:31:45 2006 UTC (13 years, 8 months ago) by golsen
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, 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_release_2008_09_29
Changes since 1.1: +2 -2 lines
Diff to previous 1.1
Bug fix in parse error message (blast outputs invalid query and database
sizes for unknown reasons, and this reports it).

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 4 19:32:00 2006 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
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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