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Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 20 00:05:41 2017 UTC (2 years, 8 months ago) by golsen
Branch: MAIN
CVS Tags: HEAD
Changes since 1.47: +204 -47 lines
Diff to previous 1.47 , to selected 1.44
Several new functions, and added cleaner names for a few commonly used
functions.

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 13 17:21:36 2017 UTC (2 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.46: +1 -1 lines
Diff to previous 1.46 , to selected 1.44
another patch for is_filehandle.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 13 21:47:47 2017 UTC (3 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.45: +1 -1 lines
Diff to previous 1.45 , to selected 1.44
update is-glob test

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 13 16:56:48 2017 UTC (3 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.44: +11 -5 lines
Diff to previous 1.44
Really commit the is-filehandle code this time.

Revision 1.44 - (view) (download) (as text) (annotate) - [selected]
Fri Jan 13 16:42:03 2017 UTC (3 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.43: +1 -1 lines
Diff to previous 1.43
Change inline ref($fh) == GLOB tests for filehandles to use a local sub is_filehandle
that is based on ref($fh) && $fh->can('print').

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 16 22:10:42 2016 UTC (3 years, 9 months ago) by golsen
Branch: MAIN
Changes since 1.42: +55 -9 lines
Diff to previous 1.42 , to selected 1.44
A varienty of enhancements, including more intuitive access to next_fasta().
A bug fix in next_fasta, making $_ local.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 2 02:34:59 2015 UTC (4 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.41: +14 -14 lines
Diff to previous 1.41 , to selected 1.44
A small anount of clean-up on molecule-type guessing.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 26 18:07:43 2015 UTC (4 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.40: +4 -0 lines
Diff to previous 1.40 , to selected 1.44
Changes copied from SEEDtk project.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 28 07:44:35 2015 UTC (5 years ago) by parrello
Branch: MAIN
Changes since 1.39: +888 -714 lines
Diff to previous 1.39 , to selected 1.44
Changes copied from SEEDtk project.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 17 18:02:54 2014 UTC (5 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.38: +3 -3 lines
Diff to previous 1.38 , to selected 1.44
Change case matching logic on genetic codes.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 29 21:59:46 2014 UTC (5 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2014_0912
Changes since 1.37: +58 -5 lines
Diff to previous 1.37 , to selected 1.44
Add sequence type guessing.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 14 21:22:31 2014 UTC (5 years, 7 months ago) by fangfang
Branch: MAIN
Changes since 1.36: +2 -2 lines
Diff to previous 1.36 , to selected 1.44
minor fix

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 20:23:18 2014 UTC (5 years, 7 months ago) by fangfang
Branch: MAIN
Changes since 1.35: +4 -2 lines
Diff to previous 1.35 , to selected 1.44
trivial changes

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 20:19:44 2014 UTC (5 years, 7 months ago) by fangfang
Branch: MAIN
Changes since 1.34: +24 -0 lines
Diff to previous 1.34 , to selected 1.44
add routines to verify sequence triples

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 16 20:33:03 2013 UTC (6 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2014_0729
Changes since 1.33: +1 -1 lines
Diff to previous 1.33 , to selected 1.44
fix an error in interpret_aa_alignment().

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 18:28:01 2013 UTC (7 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.32: +82 -0 lines
Diff to previous 1.32 , to selected 1.44
Add functions for splitting fasta titles into triples of id_def_org.
Also split NCBI nr titles on ^A.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 21 05:15:45 2013 UTC (7 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.31: +2 -2 lines
Diff to previous 1.31 , to selected 1.44
Just a documentation change.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 19:15:05 2012 UTC (7 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.30: +5 -5 lines
Diff to previous 1.30 , to selected 1.44
Some minor code changes to decrease unnecessary rewriting of sequences.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 8 18:04:04 2012 UTC (7 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.29: +63 -37 lines
Diff to previous 1.29 , to selected 1.44
Merged sets of changes in personal copy and SEED copy.
Added a few useful functions.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 30 19:24:55 2012 UTC (7 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +2 -2 lines
Diff to previous 1.28 , to selected 1.44
fixes to translation

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 13 20:47:50 2012 UTC (7 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.27: +20 -0 lines
Diff to previous 1.27 , to selected 1.44
add write_fasta as synonym for print_alignment_as_fasta

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 15 22:12:37 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_12152011, mgrast_release_3_1_2
Changes since 1.26: +2 -0 lines
Diff to previous 1.26 , to selected 1.44
Improve error handling in read_fasta.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 15 21:45:09 2011 UTC (8 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.25: +22 -12 lines
Diff to previous 1.25 , to selected 1.44
Some improvements in the fasta reader to handle Unix, Mac and Windows
return conventions.  Also, handle a raw sequence.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 5 21:23:20 2011 UTC (9 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_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_rel_2011_0928
Changes since 1.24: +14 -14 lines
Diff to previous 1.24 , to selected 1.44
Just some additions to the function descriptions.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 2 18:57:43 2011 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.23: +7 -5 lines
Diff to previous 1.23 , to selected 1.44
Some minor changes to translation with user codes (saving the ambiguous
codon translations that are encountered).

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:23:35 2010 UTC (9 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.22: +0 -1 lines
Diff to previous 1.22 , to selected 1.44
get rid of Dumper

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:18:15 2010 UTC (9 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.21: +5 -6 lines
Diff to previous 1.21 , to selected 1.44
Bug fixes in oligomer_similarity().

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 20:04:05 2010 UTC (9 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.20: +62 -0 lines
Diff to previous 1.20 , to selected 1.44
Add code for similarity at any arbitary oligo size.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 22:13:28 2010 UTC (9 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.19: +200 -20 lines
Diff to previous 1.19 , to selected 1.44
Much code clean-up and consolidation.

New version of add to alignment that does much better gap placement.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 17:29:14 2010 UTC (9 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.18: +30 -2 lines
Diff to previous 1.18 , to selected 1.44
Add a pack sequences function, and allow * in a packed sequence (stop).

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 15 23:51:00 2010 UTC (9 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.17: +32 -20 lines
Diff to previous 1.17 , to selected 1.44
Minor style updates.
Add the ability of read_fasta() to interpret a reference to a sting as
a fasta format string.
use gjoseqlib; $s=join("",<>); @seq=read_fasta(\$s); print_alignment_as_fasta(\@seq);
will echo sequences from stdin.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 18 20:01:14 2010 UTC (10 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.16: +72 -2 lines
Diff to previous 1.16 , to selected 1.44
Add new function for assessing similarity of aligned sequences.
Fix a bug in print fasta when sequence function is undefined under -w.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 24 21:22:46 2009 UTC (10 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.15: +2 -0 lines
Diff to previous 1.15 , to selected 1.44
Add more modules to the SAS toolkit.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 13 18:42:53 2009 UTC (10 years, 11 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.14: +51 -6 lines
Diff to previous 1.14 , to selected 1.44
Improve the comments and descriptions of functions.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:50:43 2009 UTC (11 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.13: +10 -17 lines
Diff to previous 1.13 , to selected 1.44
fixes to support search for rRNAs

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 12 20:08:01 2008 UTC (12 years, 1 month 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, 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_release_2008_09_29
Changes since 1.12: +1 -1 lines
Diff to previous 1.12 , to selected 1.44
Fixed major error in read_fasta() when there is not definition.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 20:37:27 2008 UTC (12 years, 1 month ago) by golsen
Branch: MAIN
Changes since 1.11: +167 -49 lines
Diff to previous 1.11 , to selected 1.44
Fix a bug in translation with user-supplied genetic code (thank you Gordon).
Fix a bug in read_next_fasta_seq() that failed when the fasta header line
had an id, a space, and then no description.
Improve flexibility of read_next_fasta_seq() so that it will take a file
name, a file handle, or default to STDIN.
Double the speed of read_fasta by reading the whole file, then splitting
it into the structures.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 3 21:36:41 2008 UTC (12 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.10: +169 -0 lines
Diff to previous 1.10 , to selected 1.44
Add routines for calculating the fractional sequence difference in a
nucleotide alignment.  They sould be much faster than a loop over
pairs of positions, and allow separate weighting of gap openning and
gap extension, and of terminal versus interal gaps.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 23 00:33:31 2007 UTC (12 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.9: +208 -215 lines
Diff to previous 1.9 , to selected 1.44
Add support for pyrrolysyl proteins.  Also, major revision and clean-up
of the translation utilities in gjoseqlib.pm.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 1 20:07:42 2007 UTC (12 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.8: +72 -6 lines
Diff to previous 1.8 , to selected 1.44
Add new subsequence subroutines.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 26 15:20:16 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +2 -1 lines
Diff to previous 1.7 , to selected 1.44
minor fixes

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 10 17:34:54 2007 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.6: +96 -3 lines
Diff to previous 1.6 , to selected 1.44
Remove dependency on gjolib.pm
Add function to read a sequencing quality score file.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 10 17:24:38 2007 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.5: +8 -2 lines
Diff to previous 1.5 , to selected 1.44
Add just a little more usage information for pack_alignment()

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 10 17:17:40 2007 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.4: +39 -0 lines
Diff to previous 1.4 , to selected 1.44
Add a pack_alignment function.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 15 00:09:52 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +597 -227 lines
Diff to previous 1.3 , to selected 1.44
add ability to insert sequences into a tree

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.2: +17 -0 lines
Diff to previous 1.2 , to selected 1.44
Added license words.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 30 18:33:41 2005 UTC (14 years, 4 months ago) by golsen
Branch: MAIN
Changes since 1.1: +476 -90 lines
Diff to previous 1.1 , to selected 1.44
This package is not currently used by any scripts, but I anticipate doing
so.  I had not been keeping the FIG version up-to-date relative to my
own.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Branch point for: initial
Diff to selected 1.44
Initial revision

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