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Author SHA1 Message Date
Celine Mercier 621b4972db Functions to get obiblobs through views 2016-11-18 15:59:50 +01:00
Celine Mercier 7d022c1a52 If the indexer name is NULL when creating a column, it now becomes the 
column name
 2016-11-18 15:56:51 +01:00
Celine Mercier 1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier 54cfeffd85 Goes with 8f724f4f, forgotten file 2016-11-10 14:48:31 +01:00
Celine Mercier a0ebc2d871 Functions to directly retrieve Obiblobs from indexers 2016-11-10 14:45:28 +01:00
Celine Mercier 8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +01:00
Celine Mercier 359578814b Added view type property to OBIView cython class and updated obi export 
to use it
 2016-11-08 17:49:59 +01:00
Celine Mercier 51b23915ca Added properties for Nuc_Seq cython classes (and updated commands using 
them)
 2016-11-08 16:59:32 +01:00
Celine Mercier b5b889c4a2 Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the 
new properties of its parent class
 2016-11-08 11:26:37 +01:00
Celine Mercier 36ac315125 Fixed bugs with python view type when creating a new view, and a bug 
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
 2016-11-08 11:23:54 +01:00
Celine Mercier 8291693309 obi grep: updated to work with the new line selection class and within 
the local sequence environment, and progress bar functioning
 2016-11-08 11:19:12 +01:00
Celine Mercier 4bc19c3e49 obi export: view type is now checked and progress bar functioning 2016-11-08 11:17:20 +01:00
Celine Mercier 2d2fe5279d Added functions to add new taxa to a taxonomy with handling of 
associated *.ldx files
 2016-11-03 17:59:21 +01:00
Celine Mercier 2504bf0fa9 Added an iterator to the OBI_Taxonomy cython class 2016-11-02 11:08:18 +01:00
Celine Mercier d8a257e711 Taxonomy handling functions in C. Features: read taxdump, read binary 
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
 2016-10-27 18:56:11 +02:00
Celine Mercier b63d0fb9fb Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a 
taxonomy C structure
 2016-10-14 17:03:10 +02:00
Celine Mercier 0dfd67ec89 The endianness of binary taxonomy files is now correctly checked 2016-10-10 17:04:29 +02:00
Celine Mercier 0faaac49cf The taxonomy directory of the DMS is now automatically created with the 
DMS
 2016-10-10 17:02:51 +02:00
Celine Mercier 1b07109e51 Removed deprecated code 2016-10-10 17:01:51 +02:00
Celine Mercier 60ab503a14 Added properties in the OBI_Taxonomy class 2016-10-10 17:01:17 +02:00
Celine Mercier 2dcfdc59fc When a new view is created with a line selection, the view to clone is 
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
 2016-10-06 17:55:18 +02:00
Celine Mercier 399fc2c051 Removed deprecated source files previously used for tests 2016-09-30 17:49:37 +02:00
Celine Mercier 9cd57deca9 Added OBIView_line_selection class to make new line selections 
associated with the view to clone, and improved and renamed method
closing a view
 2016-09-30 17:48:53 +02:00
Celine Mercier d88811ed7d Added a seed option to the obi test command for reproducible tests 2016-09-29 17:34:48 +02:00
Celine Mercier 8c402101e4 Renamed private attributes as _* and removed some deprecated code 2016-09-28 16:56:44 +02:00
Celine Mercier 1a7b42018e Added some error checking when opening or creating a view 2016-09-28 14:28:34 +02:00
Celine Mercier b717e8bb8b Added properties for the OBIView class and cleaned up deprecated code 2016-09-28 14:26:23 +02:00
Celine Mercier 03a2c8ef7c Finished restructuring the OBIDMS_column class properties 2016-09-27 14:16:30 +02:00
Celine Mercier a7f891d1c9 Added a lines_used property to the OBIDS_column class 2016-09-26 18:04:28 +02:00
Celine Mercier bd50b3f972 Added version property to OBIDMS_column class 2016-09-26 17:45:10 +02:00
Celine Mercier 81380363b7 Added original_name property to OBIDMS_column class 2016-09-26 17:31:32 +02:00
Celine Mercier a4b8349274 Added data_type property to OBIDMS_column class 2016-09-26 17:12:20 +02:00
Celine Mercier a474391b27 Added nb_elements_per_line property to OBIDMS_column class 2016-09-26 17:01:13 +02:00
Celine Mercier a0bc45cc92 Added elements_names property to OBIDMS_column class 2016-09-26 16:53:16 +02:00
Celine Mercier 76f89717fe Added alias property to OBIDMS_column cython class 2016-09-26 16:12:48 +02:00
Celine Mercier b408a4f6eb Changed file name limits to adapt to system limits + minor changes 2016-09-22 18:05:07 +02:00
Celine Mercier b083745f56 Deleted the "new line selection while editing a view" system 2016-09-22 11:19:29 +02:00
Celine Mercier 43f3c69a40 Fixed bug when cloning column with line selection 2016-09-21 17:50:21 +02:00
Celine Mercier e79507b629 Fixed bugs in the process ensuring that all the columns of a view have 
the same line count, fixed a bug when trying to set a value in a view
when a line selection exists, fixed a bug when adding a new column to a
view where line counts would be wrong
 2016-09-21 17:42:17 +02:00
Celine Mercier bb25723d99 Improved documentation of a function 2016-09-21 17:30:39 +02:00
Celine Mercier a0da984003 Fixed bug where columns would not get truncated to the right size, and 
fixed bug where column directories would be open and not closed in some
instances
 2016-09-21 17:28:52 +02:00
Celine Mercier 802bae110b Removed deprecated function 2016-09-21 17:09:59 +02:00
Celine Mercier dd55aef3e5 Added column class method to get the unique references (name and 
version) of a column
 2016-09-21 17:08:44 +02:00
Celine Mercier 9ac522fde1 Better obi test command 2016-09-21 17:06:35 +02:00
Celine Mercier 8f49553d5a First version of the obi test command, testing that the OBITools3 work 
correctly
 2016-09-15 12:26:07 +02:00
Celine Mercier 986f90c59e Fixed bug where column directories weren't closed correctly, leading to 
too many file descriptors open, and added error checking when closing
file descriptors
 2016-09-15 12:18:40 +02:00
Celine Mercier a240ec0169 Added error checking when closing file descriptors 2016-09-15 11:58:56 +02:00
Celine Mercier 0a3c23d9d0 Added a missing closedir 2016-09-15 11:58:34 +02:00
Celine Mercier 8724445fa1 Added error checking when closing files 2016-09-15 11:50:30 +02:00
Celine Mercier de189fd7e0 Fixed major bug when cloning an AVL where the bloom filter was not 
copied properly (because the sutructure copy via assignation does not
work for structures with a variable size)
 2016-09-15 11:47:02 +02:00
Celine Mercier 9a97f1f633 View predicates are now carried over when cloning a view 2016-09-06 16:22:24 +02:00
Celine Mercier 00014eb023 View files now have the *.obiview extension 2016-09-06 14:19:13 +02:00
Celine Mercier acc0da2d0b Readjusted some limits for file names and file numbers to be under OS 
limits
 2016-09-05 12:39:04 +02:00
Celine Mercier 668696fc5a Fixed major bug: when setting all the columns of a view to the same 
number of lines, columns are now cloned before being enlarged if needed
+ predicate functions now print error messages if the predicates are not
respected
 2016-09-05 12:37:36 +02:00
Celine Mercier ba84ef4847 Fixed typo 2016-09-05 12:31:06 +02:00
Celine Mercier c9dce03295 Fixed major bug when cloning an AVL group (last AVL of new group was not 
correctly enlarged before copying the data) + minor improvements
 2016-09-05 12:29:52 +02:00
Celine Mercier eb82d088cb Added some view class methods 2016-09-05 12:20:00 +02:00
Celine Mercier f46ea0b988 Finished fixing issues with DMS paths 2016-08-30 11:09:45 +02:00
Celine Mercier 5b2e370ffb Fixed a bug when using an absolute path for a DMS 2016-08-29 17:30:31 +02:00
Celine Mercier 8d360b0fac Minor improvements to obi export command 2016-08-19 17:49:22 +02:00
Celine Mercier b34769b27c Minor improvements to obi export command 2016-08-19 17:46:55 +02:00
Celine Mercier 2d0a714e37 Basic obi export command exporting from view to fasta or fastq format, 
for testing purposes
 2016-08-19 17:40:58 +02:00
Celine Mercier 7b780ffb28 View files now have a dynamic size to allow unlimited comments size 2016-08-18 17:57:03 +02:00
Celine Mercier e4129610cf Quality columns are now optional in NUC_SEQS views + minor fixes 2016-08-16 15:17:26 +02:00
Celine Mercier cf839522e7 Minor update and fix to obi grep command 2016-08-12 17:45:44 +02:00
Celine Mercier 10b22f79da The cython subclass is now correctly chosen when cloning a view 2016-08-12 17:39:19 +02:00
Celine Mercier ad8e10f2d1 Reworked a bit alignment API 2016-08-12 15:56:07 +02:00
Celine Mercier 92cad61417 Fixed bug when closing views with no associated predicate 2016-08-12 15:52:38 +02:00
Celine Mercier 64a745ce0b First very basic version of obi grep command 2016-08-11 17:32:08 +02:00
Celine Mercier 2d8ac2b035 Fixed bug when creating an OBI_IDX column 2016-08-11 17:30:32 +02:00
Celine Mercier 5b7917bb5a Fixed bug when writing predicates in view file 2016-08-11 17:30:09 +02:00
Celine Mercier d3c58780a0 Added __len__ function do OBIViews that returns the line count 2016-08-10 17:20:23 +02:00
Celine Mercier 029d395da1 Added __iter__ function to OBIView lines 2016-08-10 17:08:22 +02:00
Celine Mercier bea02cc7a5 Added (temporary?) check for the type of quality strings because the 
import now seems to return them with bytes type
 2016-08-10 16:25:45 +02:00
Celine Mercier 4ba01617af Fixed obscure compilation bug 2016-08-10 15:26:40 +02:00
Celine Mercier bec684d5e2 Fixed merge conflict 2016-08-10 15:05:37 +02:00
Celine Mercier 2aaa87edcc 1st version of obi align command and reworked functions that handle 
column alignment
 2016-08-10 14:51:02 +02:00
Celine Mercier 26b8e1f215 Modified C API to set and get in columns: added functions to set and get 
using column names instead of pointers, and changed function names
 2016-08-02 16:33:19 +02:00
Celine Mercier 312f50ff0f Major update: Column aliases. Columns are now identified in the context 
of a view by an alias that can be modified.
 2016-08-01 18:25:30 +02:00
Celine Mercier 3843485a04 Deleted deprecated function declaration that would make compilation 
impossible and fixed error in documentation
 2016-07-22 16:21:02 +02:00
Celine Mercier 20425a5d2b Deleted deprecated structure declarations 2016-07-19 15:48:56 +02:00
Celine Mercier 56e4848ebd The predicates associated with a view are now described in its comments 
field
 2016-07-19 15:31:21 +02:00
Celine Mercier 8850e40b6e Minor changes for better presentation 2016-07-19 15:30:17 +02:00
Celine Mercier b89af38109 Goes with 38718320 2016-07-18 13:57:49 +02:00
Celine Mercier 38718320f9 First version for the association of one column to another. Closes #55 2016-07-15 15:38:49 +02:00
Celine Mercier 8ee85c3005 A first version of predicate functions that are checked when a new view 
is saved and closed
 2016-07-12 14:54:11 +02:00
Celine Mercier 0869b9ba3f Closes issue #47 by storing each view in a separate file named with the 
view's name and created upon view creation.
 2016-06-30 11:41:30 +02:00
Celine Mercier ad2af0b512 Some comments updated 2016-06-16 11:26:54 +02:00
Celine Mercier 38e603ed57 Deleted some redundant cython code 2016-06-10 10:34:47 +02:00
Celine Mercier f438c3d913 OBIQUAL columns can now handle multiple elements per line 2016-06-09 15:54:36 +02:00
Celine Mercier 2a1ea3ba3f Setting NA values is now handled properly for OBI_SEQ, OBI_STR and 
OBI_QUAL columns
 2016-06-09 14:22:36 +02:00
Celine Mercier fc3641d7ff Read-only AVLs are now hard-linked instead of copied when cloning an AVL 
group to make it writable. Also fixed several bugs when handling AVL
groups.
 2016-06-03 19:02:46 +02:00
Celine Mercier 799b942017 Deleted old debugging print 2016-06-03 18:57:32 +02:00
Celine Mercier 6e3f5b230e Fixed typo in doc 2016-06-03 18:56:45 +02:00
Celine Mercier 2f57f80c63 Fixed a bug where an unmapped variable would be read 2016-06-03 18:55:58 +02:00
Celine Mercier 2962c4d250 Goes with previous commit 2016-06-03 18:54:25 +02:00
Celine Mercier 69bf7ec2e7 NA value for OBI_STR and OBI_SEQ columns is now NULL 2016-06-03 18:53:22 +02:00
Celine Mercier e681ca646d Fixed a problem with some columns being shorter in views and triggering 
errors when trying to get values. Temporary fix that needs discussion
 2016-05-20 18:45:29 +02:00
Celine Mercier 3b59043ea8 Major update: New column type to store sequence qualities. Closes #41 2016-05-20 16:45:22 +02:00
Celine Mercier ffff91e76c Fixed variable name that had been accidentally changed for better 
clarity
 2016-05-18 13:27:41 +02:00