ViewVC Help
View File | Revision Log | Show Annotations | Root Listing
root/biopy-pgml/setup.py
Links to HEAD: (view) (annotate)
Sticky Tag:
Sort logs by:
Revision 1.69 - (view) (annotate) - [select for diffs]
Wed Apr 21 21:42:48 2004 UTC (12 years ago) by chapmanb
Branch: MAIN
CVS Tags: HEAD
Changes since 1.68: +1 -0 lines
Diff to previous 1.68
*** empty log message ***

Revision 1.68 - (view) (annotate) - [select for diffs]
Fri Apr 9 02:47:51 2004 UTC (12 years ago) by chapmanb
Branch: MAIN
Changes since 1.67: +1 -0 lines
Diff to previous 1.67
*** empty log message ***

Revision 1.67 - (view) (annotate) - [select for diffs]
Thu Apr 1 22:14:07 2004 UTC (12 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.66: +1 -0 lines
Diff to previous 1.66
*** empty log message ***

Revision 1.66 - (view) (annotate) - [select for diffs]
Wed Mar 24 20:49:46 2004 UTC (12 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.65: +1 -0 lines
Diff to previous 1.65
*** empty log message ***

Revision 1.65 - (view) (annotate) - [select for diffs]
Tue Feb 17 22:14:45 2004 UTC (12 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.64: +1 -0 lines
Diff to previous 1.64
Code for placing ESTs onto genes

Revision 1.64 - (view) (annotate) - [select for diffs]
Wed Feb 4 23:09:57 2004 UTC (12 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.63: +2 -0 lines
Diff to previous 1.63
Added code to work with dating of a supplied file

Revision 1.63 - (view) (annotate) - [select for diffs]
Mon Jan 26 19:39:08 2004 UTC (12 years, 3 months ago) by chapmanb
Branch: MAIN
Changes since 1.62: +1 -0 lines
Diff to previous 1.62
Added hmmpfam for running on a cluster

Revision 1.62 - (view) (annotate) - [select for diffs]
Tue Nov 11 20:18:13 2003 UTC (12 years, 5 months ago) by chapmanb
Branch: MAIN
Changes since 1.61: +1 -0 lines
Diff to previous 1.61
Added code for calculating substitution values

Revision 1.61 - (view) (annotate) - [select for diffs]
Wed Oct 22 19:17:24 2003 UTC (12 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.60: +1 -0 lines
Diff to previous 1.60
*** empty log message ***

Revision 1.60 - (view) (annotate) - [select for diffs]
Wed Oct 8 19:00:15 2003 UTC (12 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.59: +1 -0 lines
Diff to previous 1.59
Added more parameter estimations

Revision 1.59 - (view) (annotate) - [select for diffs]
Tue Oct 7 20:54:05 2003 UTC (12 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.58: +7 -1 lines
Diff to previous 1.58
Scripts and modules for looking at various search parameters

Revision 1.58 - (view) (annotate) - [select for diffs]
Tue Aug 26 17:31:09 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.57: +2 -1 lines
Diff to previous 1.57
Code for writing out analysis results -- useful for determing parameters to set

Revision 1.57 - (view) (annotate) - [select for diffs]
Sat Aug 23 22:55:21 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.56: +2 -1 lines
Diff to previous 1.56
Added simple spreadsheet analysis output

Revision 1.56 - (view) (annotate) - [select for diffs]
Tue Aug 19 22:19:24 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.55: +3 -1 lines
Diff to previous 1.55
Started work on refactoring the duplication detection fun

Revision 1.55 - (view) (annotate) - [select for diffs]
Mon Aug 11 20:27:29 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.54: +1 -0 lines
Diff to previous 1.54
Work with expression data

Revision 1.54 - (view) (annotate) - [select for diffs]
Mon Aug 4 23:02:36 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.53: +1 -0 lines
Diff to previous 1.53
More and more gene conversion work

Revision 1.53 - (view) (annotate) - [select for diffs]
Sun Aug 3 18:10:23 2003 UTC (12 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.52: +1 -0 lines
Diff to previous 1.52
First steps at gene conversion detection

Revision 1.52 - (view) (annotate) - [select for diffs]
Fri Aug 1 19:49:36 2003 UTC (12 years, 9 months ago) by chapmanb
Branch: MAIN
Changes since 1.51: +2 -7 lines
Diff to previous 1.51
Added code for working with protein domain information on duplicates.
Removed old code for doing various things with SNPs and duplicates as it has all been replaced by the new framework. Woo.

Revision 1.51 - (view) (annotate) - [select for diffs]
Tue Jul 29 21:29:31 2003 UTC (12 years, 9 months ago) by chapmanb
Branch: MAIN
Changes since 1.50: +1 -0 lines
Diff to previous 1.50
Fixed SNP problems; started work on doing analyses on SNP information

Revision 1.50 - (view) (annotate) - [select for diffs]
Mon Jul 28 22:45:20 2003 UTC (12 years, 9 months ago) by chapmanb
Branch: MAIN
Changes since 1.49: +1 -1 lines
Diff to previous 1.49
Enough work I'm going home

Revision 1.49 - (view) (annotate) - [select for diffs]
Mon Jul 28 22:24:58 2003 UTC (12 years, 9 months ago) by chapmanb
Branch: MAIN
Changes since 1.48: +1 -0 lines
Diff to previous 1.48
First stab at new SNP stuff

Revision 1.48 - (view) (annotate) - [select for diffs]
Sat Jul 26 21:46:36 2003 UTC (12 years, 9 months ago) by chapmanb
Branch: MAIN
Changes since 1.47: +2 -0 lines
Diff to previous 1.47
Work on generalizing acces to duplicate codes

Revision 1.47 - (view) (annotate) - [select for diffs]
Wed Jun 18 20:07:47 2003 UTC (12 years, 10 months ago) by chapmanb
Branch: MAIN
Changes since 1.46: +3 -2 lines
Diff to previous 1.46
Added Script to calculate sequence size

Revision 1.46 - (view) (annotate) - [select for diffs]
Mon Jun 9 20:07:06 2003 UTC (12 years, 10 months ago) by chapmanb
Branch: MAIN
Changes since 1.45: +3 -2 lines
Diff to previous 1.45
Updated duplication comparison programs for use with rice, added configuration files instead of the crappy workarounds I have now, and updated file fetching at NCBI to use the EUtils interfaces

Revision 1.45 - (view) (annotate) - [select for diffs]
Thu May 29 19:32:57 2003 UTC (12 years, 11 months ago) by chapmanb
Branch: MAIN
Changes since 1.44: +5 -1 lines
Diff to previous 1.44
Added synonymous subsitution program with new dN figuring capabilities

Revision 1.44 - (view) (annotate) - [select for diffs]
Fri Dec 13 20:51:02 2002 UTC (13 years, 4 months ago) by chapmanb
Branch: MAIN
CVS Tags: HEAD_NEW
Changes since 1.43: +1 -0 lines
Diff to previous 1.43
New module for finding genes without introns

Revision 1.43 - (view) (annotate) - [select for diffs]
Fri Dec 13 01:20:00 2002 UTC (13 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.42: +1 -0 lines
Diff to previous 1.42
Coding work on SNP finding

Revision 1.42 - (view) (annotate) - [select for diffs]
Wed Dec 4 21:07:27 2002 UTC (13 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.41: +3 -1 lines
Diff to previous 1.41
New SNP in duplication code

Revision 1.41 - (view) (annotate) - [select for diffs]
Mon Oct 21 20:11:00 2002 UTC (13 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.40: +1 -0 lines
Diff to previous 1.40
Added analysis stuff

Revision 1.40 - (view) (annotate) - [select for diffs]
Mon Oct 21 19:48:44 2002 UTC (13 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.39: +4 -1 lines
Diff to previous 1.39
Tons of additions -- 4 way phylogenies

Revision 1.39 - (view) (annotate) - [select for diffs]
Thu Oct 10 21:10:31 2002 UTC (13 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.38: +3 -1 lines
Diff to previous 1.38
Updates to three way stuff

Revision 1.38 - (view) (annotate) - [select for diffs]
Mon Sep 16 16:20:40 2002 UTC (13 years, 7 months ago) by chapmanb
Branch: MAIN
Changes since 1.37: +6 -1 lines
Diff to previous 1.37
Updates from network downtime

Revision 1.37 - (view) (annotate) - [select for diffs]
Wed Aug 14 14:04:35 2002 UTC (13 years, 8 months ago) by chapmanb
Branch: MAIN
Changes since 1.36: +3 -1 lines
Diff to previous 1.36
Added new script for dealing with GO proteins

Revision 1.36 - (view) (annotate) - [select for diffs]
Fri Jun 7 21:09:55 2002 UTC (13 years, 10 months ago) by chapmanb
Branch: MAIN
Changes since 1.35: +2 -1 lines
Diff to previous 1.35
Added code for splitting protein distances into families and duplication regions

Revision 1.35 - (view) (annotate) - [select for diffs]
Fri May 31 21:07:10 2002 UTC (13 years, 11 months ago) by chapmanb
Branch: MAIN
Changes since 1.34: +1 -0 lines
Diff to previous 1.34
Added code for reading from TIGR XML files

Revision 1.34 - (view) (annotate) - [select for diffs]
Mon May 6 16:44:07 2002 UTC (13 years, 11 months ago) by chapmanb
Branch: MAIN
Changes since 1.33: +2 -1 lines
Diff to previous 1.33
More updates to taxonomy script plus go work

Revision 1.33 - (view) (annotate) - [select for diffs]
Sun May 5 18:19:10 2002 UTC (13 years, 11 months ago) by chapmanb
Branch: MAIN
Changes since 1.32: +2 -1 lines
Diff to previous 1.32
Added scripts for retrieving by taxonomy id from NCBI

Revision 1.32 - (view) (annotate) - [select for diffs]
Fri May 3 20:18:30 2002 UTC (14 years ago) by chapmanb
Branch: MAIN
Changes since 1.31: +1 -0 lines
Diff to previous 1.31
Added initial code for dealing with GO

Revision 1.31 - (view) (annotate) - [select for diffs]
Fri Apr 26 12:45:30 2002 UTC (14 years ago) by chapmanb
Branch: MAIN
Changes since 1.30: +2 -1 lines
Diff to previous 1.30
Updates, especially to gene family code

Revision 1.30 - (view) (annotate) - [select for diffs]
Thu Mar 28 16:07:03 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.29: +2 -0 lines
Diff to previous 1.29
Code for finding and writing out arabidopsis rice duplications works

Revision 1.29 - (view) (annotate) - [select for diffs]
Wed Mar 27 17:35:58 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.28: +2 -0 lines
Diff to previous 1.28
Added code for doing rice/arabidopsis comparisons using gene family duplications.

Revision 1.28 - (view) (annotate) - [select for diffs]
Wed Mar 27 09:20:10 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.27: +1 -0 lines
Diff to previous 1.27
Initial commit of code to client code to interact with DAS servers.

Revision 1.27 - (view) (annotate) - [select for diffs]
Mon Mar 18 16:48:18 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.26: +1 -0 lines
Diff to previous 1.26
Added code for combining duplications

Revision 1.26 - (view) (annotate) - [select for diffs]
Mon Mar 11 18:03:38 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.25: +1 -0 lines
Diff to previous 1.25
Code for detecting duplications based on family duplications, plus additions to family duplication code.

Revision 1.25 - (view) (annotate) - [select for diffs]
Thu Mar 7 19:30:25 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.24: +2 -0 lines
Diff to previous 1.24
Got basic duplication detection working. Now need to refine and tune it.

Revision 1.24 - (view) (annotate) - [select for diffs]
Tue Mar 5 19:17:09 2002 UTC (14 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.23: +4 -1 lines
Diff to previous 1.23
Updates to phylogeny work.

Revision 1.23 - (view) (annotate) - [select for diffs]
Mon Feb 18 12:51:23 2002 UTC (14 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
fixed typo with the new ArabDup package

Revision 1.22 - (view) (annotate) - [select for diffs]
Fri Feb 15 20:25:48 2002 UTC (14 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.21: +1 -0 lines
Diff to previous 1.21
New modules for examining duplications in the Arabidopsis genome.

Revision 1.21 - (view) (annotate) - [select for diffs]
Fri Feb 15 20:23:21 2002 UTC (14 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.20: +6 -1 lines
Diff to previous 1.20
Setup file changes for new modules.

Revision 1.20 - (view) (annotate) - [select for diffs]
Sat Jan 26 23:05:10 2002 UTC (14 years, 3 months ago) by chapmanb
Branch: MAIN
Changes since 1.19: +2 -0 lines
Diff to previous 1.19
Added tests for Rice web page parsing and fixed all bugs to get things working

Revision 1.19 - (view) (annotate) - [select for diffs]
Sun Dec 16 21:01:36 2001 UTC (14 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.18: +0 -11 lines
Diff to previous 1.18
Removed modules that were added to the biopython distribution.

Revision 1.18 - (view) (annotate) - [select for diffs]
Sun Dec 9 23:08:38 2001 UTC (14 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.17: +1 -0 lines
Diff to previous 1.17
Added script to locate oligomers within exons and design primers.

Revision 1.17 - (view) (annotate) - [select for diffs]
Sat Dec 8 21:08:44 2001 UTC (14 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.16: +1 -0 lines
Diff to previous 1.16
Added new script to parse out exon information

Revision 1.16 - (view) (annotate) - [select for diffs]
Sat Dec 8 20:08:21 2001 UTC (14 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.15: +1 -0 lines
Diff to previous 1.15
Added more scripts to be installed

Revision 1.15 - (view) (annotate) - [select for diffs]
Fri Dec 7 18:28:33 2001 UTC (14 years, 4 months ago) by chapmanb
Branch: MAIN
Changes since 1.14: +1 -0 lines
Diff to previous 1.14
Added Emboss stuff to the setup file

Revision 1.14 - (view) (annotate) - [select for diffs]
Tue Nov 27 07:10:46 2001 UTC (14 years, 5 months ago) by chapmanb
Branch: MAIN
Changes since 1.13: +4 -1 lines
Diff to previous 1.13
* Updated setup.py and scripts so that they aren't run from the top level directory (to prevent problems with Bio imports).
* Fixes to loading Organism so that CDSs are loaded correctly.
* Attempts to fix adding Blast ESTs, but the code is broken badly right now. Sigh.

Revision 1.13 - (view) (annotate) - [select for diffs]
Mon Nov 12 16:55:58 2001 UTC (14 years, 5 months ago) by chapmanb
Branch: MAIN
Changes since 1.12: +0 -17 lines
Diff to previous 1.12
Switched from using 4ODS from 4Suite (which is no longer being maintained) to ZODB from the Zope distribution. These are the initial changes (and tests) necessary to make this work.

Revision 1.12 - (view) (annotate) - [select for diffs]
Sat Nov 10 17:55:53 2001 UTC (14 years, 5 months ago) by chapmanb
Branch: MAIN
Changes since 1.11: +5 -2 lines
Diff to previous 1.11
Added Mojo Blast to module, and updates to Distributed Blasting stuff so that Mojo Blast can use it.

Revision 1.11 - (view) (annotate) - [select for diffs]
Sun Oct 14 20:20:36 2001 UTC (14 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.10: +1 -0 lines
Diff to previous 1.10
Added code to allow distributing BLASTs over multiple machines.

Revision 1.10 - (view) (annotate) - [select for diffs]
Fri Oct 12 04:05:44 2001 UTC (14 years, 6 months ago) by chapmanb
Branch: MAIN
Changes since 1.9: +29 -9 lines
Diff to previous 1.9
Updated setup.py file to deal with persistence

Revision 1.9 - (view) (annotate) - [select for diffs]
Sun Sep 16 13:11:41 2001 UTC (14 years, 7 months ago) by chapmanb
Branch: MAIN
Changes since 1.8: +1 -0 lines
Diff to previous 1.8
Added stuff for dealing with OvergoLabelings, including popping it into an ACeDB database and writing out info for label making.

Revision 1.8 - (view) (annotate) - [select for diffs]
Sat Sep 15 20:41:06 2001 UTC (14 years, 7 months ago) by chapmanb
Branch: MAIN
Changes since 1.7: +1 -0 lines
Diff to previous 1.7
Added AceDB to setup.py file

Revision 1.7 - (view) (annotate) - [select for diffs]
Sun Apr 29 19:17:53 2001 UTC (15 years ago) by chapmanb
Branch: MAIN
Changes since 1.6: +1 -0 lines
Diff to previous 1.6
Added GA Repair directory.

Revision 1.6 - (view) (annotate) - [select for diffs]
Sun Apr 22 17:28:55 2001 UTC (15 years ago) by chapmanb
Branch: MAIN
Changes since 1.5: +3 -0 lines
Diff to previous 1.5
Added Neural Network and Genetic Algorithm code that has been sitting on my computer. Includes Tests.

Revision 1.5 - (view) (annotate) - [select for diffs]
Sun Apr 1 22:13:03 2001 UTC (15 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.4: +1 -0 lines
Diff to previous 1.4
Added Graphics directory. Added code to render chromosomes using reportlab
code. Produces nice pdf output.

Revision 1.4 - (view) (annotate) - [select for diffs]
Fri Mar 23 02:56:30 2001 UTC (15 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.3: +2 -1 lines
Diff to previous 1.3
Added the ability to search for repeats in a sequence. this includes generation of reports based on the searches, and a test case for it all.

Revision 1.3 - (view) (annotate) - [select for diffs]
Sun Mar 11 19:42:31 2001 UTC (15 years, 1 month ago) by chapmanb
Branch: MAIN
Changes since 1.2: +4 -0 lines
Diff to previous 1.2
Modified to work with new Biopython release.

Revision 1.2 - (view) (annotate) - [select for diffs]
Mon Feb 5 03:53:19 2001 UTC (15 years, 2 months ago) by chapmanb
Branch: MAIN
Changes since 1.1: +12 -6 lines
Diff to previous 1.1
First addition of code for Hidden Markov Models. Includes other goodies like tests.

Revision 1.1.1.1 - (view) (annotate) - [select for diffs] (vendor branch)
Wed Dec 20 21:01:56 2000 UTC (15 years, 4 months ago) by chapmanb
Branch: pgml
CVS Tags: biopy-pgml_20001220
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 , to next main 1.69
Initial PGML import

Revision 1.1 - (view) (annotate) - [select for diffs]
Wed Dec 20 21:01:56 2000 UTC (15 years, 4 months ago) by chapmanb
Branch: MAIN
Branch point for: pgml
Initial revision

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