forked from bioperl/bioperl-live
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Changes
1783 lines (1415 loc) · 76 KB
/
Changes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
---------------------------------------------------------
Revision history for BioPerl core modules
---------------------------------------------------------
The comprehensive history and ongoing development of BioPerl:
http://github.com/bioperl/bioperl-live
Some of that history is also highlighted on our wiki:
http://www.bioperl.org/wiki/Change_log
http://www.bioperl.org/wiki/History_of_BioPerl
Bugs and requested features list:
https://redmine.open-bio.org/projects/bioperl
CPAN releases are branched from 'master'.
---------------------------------------------------------
1.6.924
[New features]
* Bio::Search::HSP::GenericHSP
- Bug #3370, added a "posterior_string" method to retrieve the
posterior probability lines (PP) from HMMER3 reports [fjossandon]
- Added a "consensus_string" method to retrieve the consensus
structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
* Bio::SearchIO::hmmer2
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Query Length and Hit Length are reported when the alignment
runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
* Bio::SearchIO::hmmer3
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Hit Length is reported when the alignment runs until the end
of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
- Implemented the capture of the posterior probability lines [fjossandon]
- Completed the development of NHMMER parsing, including alignments [fjossandon]
* Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
- Feature #2615, moved "_init_parse_params", "max_significance, "signif",
"min_score", "min_bits, and "hit_filter" methods from
'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
This means that the Bio::SearchIO->new() parameters '-signif', '-score',
'-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
besides Blast, instead of being ignored. Added tests for all moved methods
using HMMER outputs and run the full test suite and everything pass [fjossandon]
* Bio::SeqIO::MultiFile
- Autodetection of file format [fangly]
* Bio::Tools::GuessSeqFormat:
- Format detection from non-seekable filehandles such as STDIN [fangly]
[Bug fixes]
* Blast: Added support to changes in bl2seq from BLAST+ output, which
now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
* Phylip: Return undef in "next_aln" at file end to avoid
an infinite loop [yschensandiego]
* HMMER3: When a hit description is too long, it is truncated in
the Scores table. In those cases, the more complete description from
the Annotation line (>>) will be used [fjossandon]
* GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
since it is now used by HMMER3 format in alignments [fjossandon]
* GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
to return undef if the query/hit length is unknown (like in some
HMMER outputs), to avoid division by 0 crashes. Also "query_length"
now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
* HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
added support to multi-query reports, reduced code redundancy,
and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
* [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
* [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
* [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
* Fixed some Bio::Root::Utilities subroutines [fjossandon]
* Double-quotes on paths are needed in some places [fjossandon]
* [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
* Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
* Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
with the latest changes made in their own repositories [fjossandon]
* General synching of files with the master branch [fjossandon]
* Fixed tests failing in Windows because of using Linux commands [fjossandon]
* Closed many open filehandles that prevented temporary files deletion [fjossandon]
* Fixed broken MeSH parser [fjossandon]
* Fixed missing detection of format in SeqIO when given a -string [fangly]
1.6.923
* Major Windows support updates! [fjossandon]
* MAKER update to allow for stricter standard codon table [cjfields]
* Better support for circular sequences [fjossandon]
* Fixes for some complex location types [fjossandon]
* Address CONTIG bug in GenBank format, bug #3448 [cjfields]
* Fix bug #2978 related to BLAST report type [fjossandon]
* Deobfuscator fixes [DaveMessina]
1.6.922
* Address CPAN test failures [cjfields]
* Add BIOPROJECT support for Genbank files [hyphaltip]
* Better regex support for HMMER3 output [bosborne]
1.6.921
* Minor update to address CPAN test failures
1.6.920
* Remove Bio::Biblio and related files [carandraug]
- this cause version clashes with an independently-released
version of Bio::Biblio
1.6.910
[New features]
* Hash randomization fixes for perl 5.18.x
- Note: at least one module (Bio::Map::Physical) still has a failing test;
this is documented in bug #3446 and has been TODO'd; we will be pulling
Bio::Map and similar modules out of core into separate distributions in the
1.7.x release series [cjfields]
[New features]
* Bio::Seq::SimulatedRead
- New module to represent reads taken from other sequences [fangly]
* Bio::Root::Root
- Support of Clone::Fast as a faster cloning alternative [fangly]
* Bio::Root::IO
- Moved the format() and variant() methods from Bio::*IO modules to
Bio::Root::IO [fangly]
- Can now use format() to get the type of IO format in use [fangly]
* Bio::Tools::IUPAC
- New regexp() method to create regular expressions from IUPAC sequences
[fangly]
* Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
- Code refresh [fangly]
* Bio::DB::Taxonomy
- Added support for the Greengenes and Silva taxonomies [fangly]
* Bio::Tree::TreeFunctionsI
- get_lineage_string() represents a lineage as a string [fangly]
- add_trait() returns instead of reporting an error when the column
number is exceeded in add_trait() [fangly]
- Option to support tree leaves without trait [fangly]
- Allow ID of 0 in trait files [fangly]
* Bio::DB::Taxonomy::list
- Misc optimizations [fangly]
- Option -names of get_taxon() to help with ambiguous taxa [fangly]
* Bio::DB::Taxonomy::*
- get_num_taxa() returns the number of taxa in the database [fangly]
* Bio::DB::Fasta and Bio::DB::Qual
- support indexing an arbitrary list of files [fangly]
- user can supply an arbitrary index file name [fangly]
- new option to remove index file at the end [fangly]
* Bio::DB::Fasta
- now handles IUPAC degenerate residues [fangly]
* Bio::PrimarySeq and Bio::PrimarySeqI
- speed improvements for large sequences [Ben Woodcroft, fangly]
* Bio::PrimaryQual
- tightened and optimized quality string validation [fangly]
* Bio::SeqIO::fasta
- new method and option 'block', to create FASTA output with space
intervaled blocks (similar to genbank or EMBL) has been implemented.
- package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
in favour of the methods 'width' and 'preferred_id_type` respectively.
* Bio::FeatureIO::*
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::SeqFeature::Annotated
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::Cluster::SequenceFamily
- improved performance when using get_members with overlapping multiple
criteria
* Bio::SearchIO::hmmer3
- now supports nhmmer [bosborne]
[Bug fixes]
* [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
* [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
* [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
information was lost in a multi-result blast file [Paul Cantalupo]
* [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
total gaps [Paul Cantalupo]
* [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
* [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
when end of domain indicator is split across lines [Paul Cantalupo]
* [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
cjfields]
* [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
instances where blank lines are within sequences [cjfields]
* Bio::DB::Fasta reports correct alphabet for files with multiple sequence
types [fangly]
* Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
* [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
cjfields]
* Various fixes for Stockholm file indexing and processing [bosborne]
* Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
breaks parsing [cjfields]
* Fix case where Bio::Seq::Meta* objects with no meta information could not
be reverse-complemented [fangly]
* Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
* Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
when unsure that values will be numerical [fangly]
* Fix undef warnings in Bio::SeqIO::embl [fangly]
* Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
* Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
* Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
Sallou]
* Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
source_tag and display_name must return a string, not undef [fangly]
* Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
add_SeqFeature takes a single argument [fangly]
* Use cross-platform filenames and temporary directory in
Bio::DB::Taxonomy::flatfile [fangly]
* Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
properly identified as existing taxa in the database [fangly]
* Fix issue where a Bio::DB::Taxonomy::list object could not be created
without also passing a lineage to store [fangly]
* Prevent passing a directory to the gi2taxid option (-g) of
bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
[fangly]
* Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
* Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
* Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
object before trying to access, and no longer returns repeated sequences.
1.6.901 May 18, 2011
[Notes]
* Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
modules using Ace will also be deprecated [lds, cjfields]
* Minor bug fix release
* Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
* Address Build.PL issues when DBI is not present [hartzell]
* Skip gbxml.t and Interpro tests when modules not installed [cjfields]
* Remove deprecated code for perl 5.14.0 compat [cjfields]
* Due to schema changes and lack of support for older versions, support
for NeXML 0.9 is only (very) partially implemented.
See: https://redmine.open-bio.org/issues/3207
[Bug fixes]
* [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
docs [genehack, cjfields]
* $VERSION for CPAN/cpanm-based installs was broken; force setting of
module version from dist_version (probably not the best way to do this,
but it seems to work) [rbuels, cjfields]
1.6.900 April 14, 201
[Notes]
* This will probably be the last release to add significant features to
core modules; subsequent releases will be for bug fixes alone.
We are planning on a restructuring of core for summer 2011, potentially
as part of the Google Summer of Code. This may become BioPerl 2.0.
* Version bump represents 'just prior to v 1.7'. We may have point
releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
This code essentially is what is on the github master branch.
[New features]
* Core code updated for perl 5.12.x [cjfields, Charle Tilford]
* Bio::Tree refactor
- major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
- removal of Scalar::Util::weaken code, which was causing odd headaches
with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
* Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
many others]
* Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
[Warren Kretzschmar]
* Bio::SeqIO::gbxml
- bug 2515 - new contribution [Ryan Golhar, jhannah]
* Bio::Assembly::IO
- support for reading Maq, Sam and Bowtie files [maj]
- support for reading 454 GS Assembler (Newbler) ACE files [fangly]
- bug 2483: support for writing ACE files [Joshua Udall, fangly]
- bug 2599: support DBLINK annotation in GenBank files [cjfields]
- bug 2726: reading/writing granularity: whole scaffold or one contig
at a time [Joshua Udall, fangly]
* Bio::OntologyIO
- Added parsing of xrefs to OBO files, which are stored as secondary
dbxrefs of the cvterm [Naama Menda]
- General Interpro-related code refactors [dukeleto, rbuels, cjfields]
* PAML code updated to work with PAML 4.4d [DaveMessina]
[Bug fixes]
* [3198] - sort tabular BLAST hits by score [DaveMessina]
* [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
* [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
* [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
[cjfields]
* [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
* [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
* [3164] - TreeFunctionsI syntax bug [gjuggler]
* [3163] - AssemblyIO speedup [fangly]
* [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
hyphaltip]
* [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
* [3158] - fix EMBL file mis-parsing [cjfields]
* [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
cjfields]
* [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
* [3148] - URL change for UniProt [cjfields]
* [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
* [3136] - HMMer3 parser fixes [kblin]
* [3126] - catch description [Toshihiko Akiba]
* [3122] - Catch instances where non-seekable filehandles were being
seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
* [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
[dukeleto, rbuels, cjfields]
* [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
jhannah]
* [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
* [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
cjfields]
* [3107] - BLAST alignment column_from_residue_number() [cjfields]
* [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
* [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
* [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
* [3086] - EMBL misparsing long tags [kblin, cjfields]
* [3085] - CommandExts and array of files [maj, hyphaltip]
* [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
for alignment slices [Ha X. Dang, cjfields]
* [3076] - XMFA alignment strand wrong [Ha X., cjfields]
* [3073] - fix parsing of GenBank files from RDP [cjfields]
* [3068] - FASTQ parse failure with trailing 0 [cjfields]
* [3064] - All-gap midline BLAST report issues [cjfields]
* [3063] - BLASt report RID [Razi Khaja, cjfields]
* [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
* [3053] - LOCUS line formatting [M. Wayne, cjfields]
* [3039] - correct Newick output root node branch length [gjuggler,
DaveMessina]
* [3038] - SELEX alignment error [Bernd, cjfields]
* [3033] - PrimarySeq ID setting [Bernd, maj]
* [3032] - Fgenesh errors [Wes Barris, hyphaltip]
* [3034] - AlignIO::clustal output [Bernd, DaveMessina]
* [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
* [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
* [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
* [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
PAML 4.4d [DaveMessina]
* [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
DaveMessina]
* [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
* [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
* [3017] - using threads with Bio::DB::GenBank [cjfields]
* [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
* [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
* [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
* [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
* [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
cjfields]
* [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
* [2977] - TreeIO issues [DaveMessina]
* [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
* [2944] - Bio::Tools::GFF score [cjfields]
* [2942] - correct MapTiling output [maj]
* [2939] - PDB residue insertion codes [John May, maj]
* [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
* [2928] - GuessSeqFormat raw [maj]
* [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
* [2922] - open() directive issue [cjfields]
* [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
* [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
* [2899] - SeqFeature::Store host issues [lstein, dbolser]
* [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
cjfields]
* [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
* [2876] - CDD search with RemoteBlast [Malcolm Cook]
* [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
* [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
* [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
* [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
* [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
* [2758] - Bio::AssemblyIO ace problems [fangly]
* [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
* [2726] - ace file IO [Josh, fangly]
* [2700] - Refactor Build.PL [cjfields]
* [2673] - addition of simple Root-based clone() method [cjfields]
* [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
* [2599] - support for DBLINK annotation in GenBank files [cjfields]
* [2594] - Bio::Species memory leak [cjfields]
* [2515] - GenBank XML parser [jhannah]
* [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
* [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
* [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
cjfields]
* [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
[Deprecated]
* Bio::Expression modules - these were originally designed to go with the
bioperl-microarray suite of tools, however they have never been completed
and so have been removed from the distribution. The original code has
been moved into the inactive bioperl-microarray suite. [cjfields]
[Other]
* Repository moved from Subversion (SVN) to
http://github.com/bioperl/bioperl-live [cjfields]
* Bug database has moved to Redmine (https://redmine.open-bio.org)
* Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
Thieme have been moved to their own distribution (Bio-Microarray).
[cjfields]
1.6.1 Sept. 29, 2009 (point release)
* No change from last alpha except VERSION and doc updates [cjfields]
1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
* Fix for silent OBDA bug related to FASTA validation [cjfields]
1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
* Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
* [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
[cjfields]
* BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
* WinXP test fixes [cjfields, maj]
* BioPerl.pod added for descriptive information, fixes CPAN indexing
[cjfields]
* Minor doc fixes [cjfields]
1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
* Fix tests failing due to merging issues [cjfields]
* More documentation updates for POD parsing [cjfields]
1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
* Bio::Root::Build
- fix YAML meta data generation [cjfields]
1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
* Bio::Align::DNAStatistics
- fix divide by zero problem [jason]
* Bio::AlignIO::*
- bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::AlignIO::stockholm
- bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::Assembly::Tools::ContigSpectrum
- function to score contig spectrum [fangly]
* Bio::DB::EUtilities
- small updates [cjfields]
* Bio::DB::Fasta
- berkeleydb database now autoindexes wig files and locks correctly
[lstein]
* Bio::DB::HIV
- various small updates for stability; tracking changes to LANL
database interface [maj]
* Bio::DB::SeqFeature (lots of updates and changes)
- add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
- bug 2835 - patch [Dan Bolser]
- bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
* Bio::DB::SwissProt
- bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
* Bio::Factory::FTLocationFactory
- mailing list bug fix [cjfields]
* Bio::LocatableSeq
- performance work on column_from_residue_number [hartzell]
* Bio::Matrix::IO::phylip
- bug 2800 - patch to fix phylip parsing [Wei Zou]
* Bio::Nexml
- Google Summer of Code project from Chase Miller - parsers for Nexml
file format [maj, chmille4]
* Bio::PopGen
- Make Individual, Population, Marker objects AnnotatableI [maj]
- simplify LD code [jason]
* Bio::RangeI
- deal with empty intersection [jason]
* Bio::Restriction
- significant overhaul of Bio::Restriction system: complete support for
external and non-palindromic cutters. [maj]
* Bio::Root::Build
- CPANPLUS support, no automatic installation [sendu]
* Bio::Root::IO
- allow IO::String (regression fix) [cjfields]
- catch unintentional undef values [cjfields]
- throw if non-fh is passed to -fh [maj]
* Bio::Root::Root/RootI
- small debugging and core fixes [cjfields]
* Bio::Root::Test
- bug RT 48813 - fix for Strawberry Perl bug [kmx]
* Bio::Root::Utilities
- bug 2737 - better warnings [cjfields]
* Bio::Search
- tiling completely refactored, HOWTO added [maj]
NOTE : Bio::Search::Hit::* classes do not use this code directly; we
will deprecate usage of the older tiling code in the next BioPerl
release
- small fixes [cjfields]
* Bio::SearchIO
- Infernal 1.0 output now parsed [cjfields]
- new parser for gmap -f9 output [hartzell]
- bug 2852 - fix infinite loop in some output [cjfields]
- blastxml output now passes all TODO tests [cjfields]
- bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
- RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
- bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
* Bio::Seq::LargePrimarySeq
- delete tempdirs [cjfields]
- bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
* Bio::Seq::Quality
- extract regions based on quality threshold value [Dan Bolser, heikki]
- bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
* Bio::SeqFeature::Lite
- various Bio::DB::SeqFeature-related fixes [lstein]
* Bio::SeqFeature::Tools::TypeMapper
- additional terms for GenBank to SO map [scain]
* Bio::SeqIO::chadoxml
- bug 2785 - patch to get this working for bp_seqconvert [cjfields]
* Bio::SeqIO::embl
- support for CDS records [dave_messina, Sylvia]
* Bio::SeqIO::fastq
- complete refactoring to handle all FASTQ variants, perform validation,
write output. API now conforms with other Bio* parsers and the rest of
Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
[cjfields]
* Bio::SeqIO::genbank
- bug 2784 - fix DBSOURCE issue [Phillip Garland]
- bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
* Bio::SeqIO::largefasta
- parser returns a Bio::Seq::LargePrimarySeq [jhannah]
* Bio::SeqIO::raw
- add option for 'single' and 'multiple'
* Bio::SeqIO::scf
- bug 2881 - fix scf round-tripping [Adam Søgren]
* Bio::SeqUtils
- bug 2766, 2810 - copy over tags from features, doc fixes [David
Jackson]
* Bio::SimpleAlign
- bug 2793 - patch for add_seq index issue [jhannah, maj]
- bug 2801 - throw if args are required [cjfields]
- bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
[Tristan Lefebure, maj]
- bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
- fix POD and add get_SeqFeatures filter [maj]
* Bio::Tools::dpAlign
- add support for LocatableSeq [ymc]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::EUtilities
- fix for two bugs from mail list [Adam Whitney, cjfields]
- add generic ItemContainerI interface for containing same methods
[cjfields]
* Bio::Tools::HMM
- fix up code, add more warnings [cjfields]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::Primer3
- bug 2862 - fenceposting issue fixed [maj]
* Bio::Tools::Run::RemoteBlast
- tests for remote RPS-BLAST [mcook]
* Bio::Tools::SeqPattern
- bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
* Bio::Tools::tRNAscanSE
- use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
* Bio::Tree::*
- bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
* Bio::Tree::Statistics
- several methods for calculating Fitch-based score, internal trait
values, statratio(), sum of leaf distances [heikki]
* Bio::Tree::Tree
- bug 2869 - add docs indicating edge case where nodes can be
prematurely garbage-collected [cjfields]
- add as_text() function to create Tree as a string in specified format
[maj]
* Bio::Tree::TreeFunctionsI
- bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
Lefebure, maj]
* Bio::TreeIO::newick
- fix small semicolon issue [cjfields]
* scripts
- update to bp_seqfeature_load for SQLite [lstein]
- hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
- fastam9_to_table - fix for MPI output [jason]
- gccalc - total stats [jason]
* General Stuff
- POD cleanup re: FEEDBACK section [maj, cjfields]
- cleanup or fix dead links [cjfields]
- Use of no_* methods (indicating 'number of something') is deprecated
in favor of num_* [cjfields]
- lots of new tests for the above bugs and refactors [everyone!]
- new template for Komodo text editor [cjfields]
1.6.0 Winter 2009
* Feature/Annotation rollback
- Problematic changes introduced prior to the 1.5 release have been
rolled back. These changes led to subtle bugs involving operator
overloading and interface methods.
- Behavior is very similar to that for BioPerl 1.4, with tag values
being stored generically as simple scalars. Results in a modest
speedup.
* Bio::Graphics
- Split into a separate distribution on CPAN, primarily so development
isn't reliant on a complete BioPerl release.
- Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
is only available via Subversion (via bioperl-live main trunk)
* Bio::Root::Test
- Common test bed for all BioPerl modules
* Bio::Root::Build
- Common Module::Build-based subclass for all BioPerl modules
* Bio::DB::EUtilities
- Complete refactoring to split up parsing (Bio::Tools::EUtilities),
parameter handling (Bio::Tools::EUtilities::EUtilParameters),
and user agent request posting and retrieval
* Test implementation and reorganization
- Tests have been reorganized into groups based on classes or use
cases.
- Automated test coverage is now online:
http://www.bioperl.org/wiki/Test_Coverage
- After this release, untested modules will be moved into a
separate developer distribution until tests can be derived.
Also, new modules to be added are expected to have a test suite
and adequate test coverage.
1.5.2 Developer release
Full details of changes since 1.5.1 are available online at:
http://www.bioperl.org/wiki/Change_log
The following represents a brief overview of the most important changes.
o Bio::Map
- Overhaul. Brand new system fully allows markers to have multiple
positions on multiple maps, and to have relative positions. Should be
backward compatible.
o Bio::Taxonomy
- This module and all the modules in the Taxonomy directory now
deprecated in favour of Bio::Taxon and Bio::Tree::Tree
o Bio::DB::Taxonomy
- Taxonomy.pm
* get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
* New methods ancestor(), each_Descendent() and _handle_internal_id().
* Allows for different database modules to create Bio::Taxon objects
with the same internal id when the same taxon is requested from each.
- flatfile.pm
* get_Children_Taxids() is deprecated, superceded by each_Descendent().
* No longer includes the fake root node 'root'; there are multiple roots
now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
- entrez.pm
* get_node() has new option -full
* Caches data retrieved from website
o Bio::Species
- Now a Bio::Taxon. Carries out the species name -> specific name munging
that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
backward compatability in species() method.
o Bio::Search and Bio::SearchIO
- Overhaul. The existing system has been sped up via some minor changes
(mostly gain-of-function to the API). Bio::PullParserI is introduced
as a potential eventual replacment for the existing system, though as
yet only a Hmmpfam parser exists written using it.
1.5.1 Developer release
o Major problem with how Annotations were written out with
Bio::Seq is fixed by reverting to old behavior for
Bio::Annotation objects.
o Bio::SeqIO
- genbank.pm
* bug #1871; REFLOOP' parsing loop, I changed the pattern to
expect at l east 9 spaces at the beginning of a line to
indicate line wrapping.
* Treat multi-line SOURCE sections correctly, this defect broke
both common_name() and classification()
* parse swissprot fields in genpept file
* parse WGS genbank records
- embl.pm
* Changed regexp for ID line. The capturing parentheses are
the same, the difference is an optional repeated-not-semi-
colon expression following the captured \S+. This means the
regexp works when the division looks like /PRO;/ or when the
division looks like /ANG ;/ - the latter is from EMBL
repbase
* fix ID line parsing: the molecule string can have spaces in
it. Like: "genomic DNA"
- swiss.pm: bugs #1727, #1734
- entrezgene.pm
* Added parser for entrezgene ASN1 (text format) files.
Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
o Bio::AlignIO
- maf.pm coordinate problem fixed
o Bio::Taxonomy and Bio::DB::Taxonomy
- Parse NCBI XML now so that nearly all the taxonomy up-and-down
can be done via Web without downloading all the sequence.
o Bio::Tools::Run::RemoteBlast supports more options and complies
to changes to the NCBI interface. It is reccomended that you
retrieve the data in XML instead of plain-text BLAST report to
insure proper parsing and retrieval of all information as NCBI
fully expects to change things in the future.
o Bio::Tree and Bio::TreeIO
- Fixes so that re-rooting a tree works properly
- Writing out nhx format from a newick/nexus file will properly output
bootstrap information. The use must move the internal node labels over
to bootstraps.
for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
$node->bootstrap($node->id);
$node->id('');
}
- Nexus parsing is much more flexible now, does not care about
LF.
- Cladogram drawing module in Bio::Tree::Draw
- Node height and depth now properly calculated
- fix tree pruning algorithm so that node with 1 child gets merged
o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
bugs and improvements were added, see Gbrowse mailing list for most of
these.
o Bio::DB::GFF partially supports GFF3. See information about
gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
o Better location parsing in Bio::Factory::FTLocationFactory -
this is part of the engine for parsing EMBL/GenBank feature table
locations. Nested join/order-by/complement are allowed now
o Bio::PrimarySeqI->translate now takes named parameters
o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
reconstruction) is now supported. Parsing different models and
branch specific parametes are now supported.
o Bio::Factory::FTLocationFactory - parse hierarchical locations
(joins of joins)
o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
for getter/setter functions
o Bio::SearchIO
- blast bug #1739; match scientific notation in score
and possible e+ values
- blast.pm reads more WU-BLAST parameters and parameters, match
a full database pathname,
- Handle NCBI WEB and newer BLAST formats specifically
(Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
- psl off-by-one error fixed
- exonerate parsing much improved, CIGAR and VULGAR can be parsed
and HSPs can be constructed from them.
- HSPs query/hit now have a seqdesc field filled out (this was
always available via $hit->description and
$result->query_description
- hmmer.pm can parse -A0 hmmpfam files
- Writer::GbrowseGFF more customizeable.
o Bio::Tools::Hmmpfam
make e-value default score displayed in gff, rather than raw score
allow parse of multiple records
1.5 Developer release
o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
provide Jukes-Cantor and Kimura pairwise distance methods,
respectively.
o Bio::AlignIO support for "po" format of POA, and "maf";
Bio::AlignIO::largemultifasta is a new alternative to
Bio::AlignIO::fasta for temporary file-based manipulation of
particularly large multiple sequence alignments.
o Bio::Assembly::Singlet allows orphan, unassembled sequences to
be treated similarly as an assembled contig.
o Bio::CodonUsage provides new rare_codon() and probable_codons()
methods for identifying particular codons that encode a given
amino acid.
o Bio::Coordinate::Utils provides new from_align() method to build
a Bio::Coordinate pair directly from a
Bio::Align::AlignI-conforming object.
o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
web service using standard Pubmed query syntax, and retrieve
results as XML.
o Bio::DB::GFF has various sundry bug fixes.
o Bio::FeatureIO is a new SeqIO-style subsystem for
writing/reading genomic features to/from files. I/O classes
exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
classes only read/write Bio::SeqFeature::Annotated objects.
Notably, the GFF v3 class requires features to be typed into the
Sequence Ontology.
o Bio::Graph namespace contains new modules for manipulation and
analysis of protein interaction graphs.
o Bio::Graphics has many bug fixes and shiny new glyphs.
o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
indexing for HMMER reports and FASTA qual files, respectively.
o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
new objects that can be placed within a Bio::Map::MapI-compliant
genetic/physical map; Bio::Map::Physical provides a new physical
map type; Bio::MapIO::fpc provides finger-printed clone mapping
import.
o Bio::Matrix::PSM provide new support for postion-specific
(scoring) matrices (e.g. profiles, or "possums").
o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
be instantiated without explicitly using Bio::OntologyIO. This
is possible through changes to Bio::Ontology::OntologyStore to
download ontology files from the web as necessary. Locations of
ontology files are hard-coded into
Bio::Ontology::DocumentRegistry.
o Bio::PopGen includes many new methods and data types for
population genetics analyses.
o New constructor to Bio::Range, unions(). Given a list of
ranges, returns another list of "flattened" ranges --
overlapping ranges are merged into a single range with the
mininum and maximum coordinates of the entire overlapping group.
o Bio::Root::IO now supports -url, in addition to -file and -fh.
The new -url argument allows one to specify the network address
of a file for input. -url currently only works for GET
requests, and thus is read-only.
o Bio::SearchIO::hmmer now returns individual Hit objects for each
domain alignment (thus containing only one HSP); previously
separate alignments would be merged into one hit if the domain
involved in the alignments was the same, but this only worked
when the repeated domain occured without interruption by any
other domain, leading to a confusing mixture of Hit and HSP
objects.
o Bio::Search::Result::ResultI-compliant report objects now
implement the "get_statistics" method to access
Bio::Search::StatisticsI objects that encapsulate any
statistical parameters associated with the search (e.g. Karlin's
lambda for BLAST/FASTA).
o Bio::Seq::LargeLocatableSeq combines the functionality already
found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
o Bio::SeqFeature::Annotated is a replacement for
Bio::SeqFeature::Generic. It breaks compliance with the
Bio::SeqFeatureI interface because the author was sick of
dealing with untyped annotation tags. All
Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
compliant, and accessible through Bio::Annotation::Collection.
o Bio::SeqFeature::Primer implements a Tm() method for primer
melting point predictions.
o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
o Bio::Taxonomy::Node now implements the methods necessary for
Bio::Species interoperability.
o Bio::Tools::CodonTable has new reverse_translate_all() and
make_iupac_string() methods.
o Bio::Tools::dpAlign now provides sequence profile alignments.
o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
parsers.
o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
for designing small inhibitory RNA.
o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
methods based on a distance matrix.
o Bio::Tree::Statistics provides an assess_bootstrap() method to
calculate bootstrap support values on a guide tree topology,
based on provided bootstrap tree topologies.
o Bio::TreeIO now supports the Pagel (PAG) tree format.
1.4 branch
1.4.1
o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
o Bio::Graphics will work with gd1 or gd2
o Bio::SearchIO
- hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
(RF lines alone)
- blast.pm Parse multi-line query fields properly
- small speed improvements to blasttable.pm and others
o Bio::DB::Taxonomy has better support for hierarchy traversal so that
Bio::Taxonomy::Node can be as simple as Bio::Species object while still
supporting more complex queries
1.4. Stable major release
Since initial 1.2.0, 3000 separate changes have been made to make this release.
o installable scripts
o global module version from Bio::Root:Version
o Bio::Graphics
- major improvements; SVG support
o Bio::Popgen
- population genetics
- support several population genetics types of questions.
- Tests for statistical neutrality of mutations
(Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
Tests of population structure (Wright's F-statistic: Fst) is in
Bio::PopGen::PopStats. Calculating composite linkage
disequilibrium (LD) is available in Bio::PopGen::Statistics as
well.
- Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
and csv (comma delimited formatted) data.
- a directory for implementing population simulations has
been added Bio::PopGen::Simulation and 2 simulations - a
Coalescent and a simple single-locus multi-allele genetic drift
simulation have been provided. This replaces the code in
Bio::Tree::RandomTree which has been deprecated until proper
methods for generating random phylogenetic trees are
implemented.
o Bio::Restriction
- new restrion analysis modules
o Bio::Tools::Analysis
- web based DNA and Protein analysis framework and several
implementations
o Bio::Seq::Meta
- per residue annotable sequences
o Bio::Matrix
- Bio::Matrix::PSM - Position Scoring Matrix
- Bio::Matrix::IO has been added for generalized parsing of
matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
initial implementations for parsing BLOSUM/PAM and Phylip
Distance matricies respectively. A generic matrix
implementation for general use was added in
Bio::Matrix::Generic.
o Bio::Ontology
- major changes
o Bio:Tree
o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
- small inhibitory RNA
o Bio::SeqFeature::Tools
- seqFeature mapping tools