[bip] pygr0.7beta3 released
Christopher Lee
leec at chem.ucla.edu
Mon Sep 24 17:46:35 PDT 2007
Hi,
pygr0.7beta3 is available on SourceForge. This is mostly performance
improvements and bug fixes, plus some additional documentation. Some
new features include axtNet pairwise alignment format reading for
NLMSA, new_annotation() method, a Makefile for building a pure C
library version of intervaldb (libnclist), and automatic
transmission / reconstruction of seqDict info via NLMSA dump_textfile
() / textfile_to_binaries() and pygr.Data. This is very close to the
final release for version 0.7. A little bit more bug fixing is all
that's left. Please send us bug reports (specifically how to
reproduce the bug) if you have any!
Yours with best wishes,
Chris
REVISIONS SINCE beta2 release:
classutil.py
----------------------------
revision 1.13
date: 2007/08/24 05:32:25; author: leec; state: Exp; lines: +33 -1
added shadowClass support. Must pickle itself as the original class...
----------------------------
cnestedlist.pyx:
----------------------------
revision 1.87
date: 2007/09/24 22:01:16; author: leec; state: Exp; lines: +10 -3
added verbose option to dump_textfile()
----------------------------
revision 1.86
date: 2007/09/24 18:20:41; author: deepreds; state: Exp; lines: +2 -0
if maxlen is None:
maxlen=C_int_max-65536 # C_int_max MAXIMUM VALUE REPRESENTABLE
BY int
if axtFiles is not None:
maxlen = maxlen/2
maxlen reduced by half for axtNet format reading (default action).
----------------------------
revision 1.85
date: 2007/09/21 21:58:30; author: deepreds; state: Exp; lines: +3 -2
minor bug fixed when determining src_prefix / dest_prefix.
os.path.basename added
----------------------------
revision 1.84
date: 2007/09/19 19:44:15; author: leec; state: Exp; lines: +17 -12
added bidirectionalityRule option to NLMSA.__init__() to allow
direct user control of axtNet directionality rule
----------------------------
revision 1.83
date: 2007/09/19 04:33:25; author: leec; state: Exp; lines: +14 -13
made readAxtNet() handle the is_bidirectional internal setting to remove
duplicate mappings
----------------------------
revision 1.82
date: 2007/09/18 18:02:05; author: deepreds; state: Exp; lines: +1 -1
warning message changed for axtNet input file name.
----------------------------
revision 1.81
date: 2007/09/18 01:10:26; author: leec; state: Exp; lines: +20 -18
fixed axtnet saving by redirecting results to virtual LPO instead of
union
----------------------------
revision 1.80
date: 2007/09/17 21:49:16; author: deepreds; state: Exp; lines:
+38 -43
code cleaning & debugging axtNet reading function.
----------------------------
revision 1.79
date: 2007/09/14 01:39:25; author: deepreds; state: Exp; lines:
+41 -27
module to read axtNet pairwise alignment has been added.
MAF: cnestedlist.NLMSA('test', 'w', uniondict, mafFiles = maflist)
AXTNET: cnestedlist.NLMSA('test', 'w', uniondict, axtFiles = axtlist)
readMAFrecord function error fixed when reading large lines (>32767).
----------------------------
revision 1.78
date: 2007/09/06 19:07:43; author: deepreds; state: Exp; lines: +1 -0
textfile_to_binaries: import seqdb, seqDict = seqdb.PrefixUnionDict
(prefixDict)
----------------------------
revision 1.77
date: 2007/09/06 02:11:17; author: leec; state: Exp; lines: +1 -1
added trypath support to nlmsa_utils.read_seq_dict()
----------------------------
revision 1.76
date: 2007/09/06 01:52:52; author: leec; state: Exp; lines: +83 -39
added saving / loading of seqDict info to textfile
----------------------------
revision 1.75
date: 2007/09/06 00:31:13; author: leec; state: Exp; lines: +2 -1
altered warning message for saveSeqDict issue
----------------------------
revision 1.74
date: 2007/08/31 17:56:00; author: deepreds; state: Exp; lines: +3 -2
dump_textfile, .attrDict backward compatibility issue fixed.
----------------------------
revision 1.73
date: 2007/08/31 02:31:44; author: leec; state: Exp; lines: +111 -3
added readAxtnet() method for calling axtnet reading C function...
----------------------------
revision 1.72
date: 2007/08/31 00:57:54; author: leec; state: Exp; lines: +4 -1
made NLMSA.attrDict reading optional for backwards compatibility
----------------------------
revision 1.71
date: 2007/08/31 00:51:35; author: leec; state: Exp; lines: +166 -95
changed use_virtual_lpo to pairwiseMode, implemented proper try:
finally checks
----------------------------
revision 1.70
date: 2007/08/30 23:05:32; author: leec; state: Exp; lines: +23 -16
modified self culling to retain non-identical matches to self
cleaned up readMAFfiles error handling
----------------------------
revision 1.69
date: 2007/08/22 08:04:12; author: leec; state: Exp; lines: +17 -3
fuse 1:1 intervals (mergeIntervals) where possible
----------------------------
revision 1.68
date: 2007/08/22 04:24:00; author: leec; state: Exp; lines: +86 -27
added filterList option to groupByIntervals(), efficient masking and
saving of 1:1
mergeIntervals
Data.py
----------------------------
revision 1.41
date: 2007/08/24 05:31:18; author: leec; state: Exp; lines: +29 -12
made getResource cache schema information for loaded objects
also switched over to shadowClass mechanism for binding attributes:
don't bind to the original class, but instead create a shadow
subclass just for that
instance. Guarantees no possibility of schema collisions on
different objects that
use the same itemClass etc.
----------------------------
default.h
----------------------------
revision 1.4
date: 2007/09/24 23:05:02; author: leec; state: Exp; lines: +44 -2
added support for BUILD_C_LIBRARY mode, that builds a pure C library
with no
python extension module functionality
----------------------------
nlmsa_utils.py
----------------------------
revision 1.10
date: 2007/09/19 19:43:17; author: leec; state: Exp; lines: +9 -0
added prune_self_mappings() for handling axtNet directionality rule
----------------------------
revision 1.9
date: 2007/09/14 01:39:25; author: deepreds; state: Exp; lines: +2 -0
module to read axtNet pairwise alignment has been added.
MAF: cnestedlist.NLMSA('test', 'w', uniondict, mafFiles = maflist)
AXTNET: cnestedlist.NLMSA('test', 'w', uniondict, axtFiles = axtlist)
readMAFrecord function error fixed when reading large lines (>32767).
----------------------------
revision 1.8
date: 2007/09/06 02:10:43; author: leec; state: Exp; lines: +1 -1
adding trypath support
----------------------------
revision 1.7
date: 2007/09/06 01:53:26; author: leec; state: Exp; lines: +31 -0
moved read_seq_dict() and save_seq_dict() here from cnestedlist.pyx
----------------------------
revision 1.6
date: 2007/08/31 00:52:04; author: leec; state: Exp; lines: +1 -1
changed to init_pairwise_mode() call
----------------------------
seqdb.py
----------------------------
revision 1.113
date: 2007/09/18 01:12:30; author: leec; state: Exp; lines: +15 -1
added support for seqDict iteritemlen over XMLRPC
----------------------------
revision 1.112
date: 2007/08/31 07:42:24; author: leec; state: Exp; lines: +28 -10
bug fixes to new_annotation()
extended SeqPrefixUnionDict to infer prefix from db.filepath
----------------------------
revision 1.111
date: 2007/08/31 05:47:51; author: leec; state: Exp; lines: +18 -3
added AnnotationDB.new_annotation() method and __setitem__ error message
----------------------------
revision 1.110
date: 2007/08/31 01:06:56; author: leec; state: Exp; lines: +1 -1
handle TypeError raised by shelve on integer keys
----------------------------
revision 1.109
date: 2007/08/31 00:52:56; author: leec; state: Exp; lines: +1 -1
changed use_virtual_lpo to pairwiseMode
----------------------------
sequence.py
----------------------------
revision 1.33
date: 2007/08/28 20:40:51; author: calpan; state: Exp; lines: +3 -1
handle empty segment in Seq2SeqEdge.longestSegment()
----------------------------
revision 1.32
date: 2007/08/22 04:24:56; author: leec; state: Exp; lines: +17 -16
added saving of 1:1 matchIntervals on Seq2SeqEdge
----------------------------
xnestedlist.py
----------------------------
revision 1.6
date: 2007/08/31 00:50:22; author: leec; state: Exp; lines: +9 -1
make XMLRPC NLMSA properly handle EmptySliceError
----------------------------
Documentation:
----------------------------
revision 1.50
date: 2007/09/24 23:21:27; author: leec; state: Exp; lines: +1 -1
fixed typo
----------------------------
revision 1.49
date: 2007/09/24 23:12:28; author: leec; state: Exp; lines: +67 -0
added C library documentation
----------------------------
revision 1.48
date: 2007/09/24 22:11:27; author: leec; state: Exp; lines: +4 -1
added another verbose option to docs
----------------------------
revision 1.47
date: 2007/09/24 22:04:11; author: leec; state: Exp; lines: +98 -22
added docs on axtFiles reading, seqDict handling in dump_textfiles()
etc.
----------------------------
revision 1.46
date: 2007/09/24 18:30:58; author: deepreds; state: Exp; lines: +7 -6
NamedSequence -> Sequence in pygr.sequence module
----------------------------
revision 1.45
date: 2007/08/31 07:45:06; author: leec; state: Exp; lines: +27 -19
added new_annotation() docs, and changed to pairwiseMode
----------------------------
TEST REVISIONS SINCE beta2
blast_test.py
----------------------------
revision 1.6
date: 2007/08/29 14:44:23; author: deepreds; state: Exp; lines: +2 -2
data saved in another pickle file
----------------------------
revision 1.5
date: 2007/08/29 14:39:11; author: deepreds; state: Exp; lines: +1 -1
pickle opened as 'w' mode instead of 'a' mode
----------------------------
revision 1.4
date: 2007/08/29 00:06:41; author: calpan; state: Exp; lines: +5 -2
*** empty log message ***
----------------------------
revision 1.3
date: 2007/08/28 20:51:07; author: calpan; state: Exp; lines: +20 -15
updated all_v_all_blast_test result construction
----------------------------
revision 1.2
date: 2007/08/20 20:27:15; author: calpan; state: Exp; lines: +5 -6
Moved string conversion from after test to before.
----------------------------
pygrdata_test.py
----------------------------
revision 1.10
date: 2007/08/31 00:52:21; author: leec; state: Exp; lines: +2 -2
changed use_virtual_lpo to pairwiseMode
----------------------------
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