73bca6288f
New obi uniq
Celine Mercier
2017-08-20 18:04:21 +02:00
6a2759eee6
obi import with new input/ouput API
Celine Mercier
2017-08-20 17:58:36 +02:00
38029b1f77
Forgot a ;
Celine Mercier
2017-08-20 17:56:18 +02:00
663a1a1091
Cython API: column elements: added possibility to check if an element exists from its index, and a dict-like get() method
Celine Mercier
2017-08-20 17:44:05 +02:00
c6d5436a58
Cython API: fixed a bug where iteration on a NUC_SEQS view would not be done correctly (bug appeared with optimization modifications done lately)
Celine Mercier
2017-08-20 17:41:41 +02:00
47cad285d6
Cython API: fixed 2 little bugs in Seq API
Celine Mercier
2017-08-20 17:39:30 +02:00
74f15d1a23
Cython API: Various fixes in input handlers (parsers, openers etc). Mostly working but not bug-free
Celine Mercier
2017-08-20 17:37:51 +02:00
c559ddf487
BUG FIX: creation of a new column would fail because of a case not handled when a high number of elements per line would imply less than one line per memory page
Celine Mercier
2017-08-20 17:30:23 +02:00
93cff94e7f
Fixed some compilation warnings
Celine Mercier
2017-08-20 17:25:58 +02:00
9744a48a67
BUG FIX: seemingly identical obiblobs would have different hash values because of the padding added by the compiler. Fixed by using calloc instead of malloc for obiblob memory allocation.
Celine Mercier
2017-08-20 17:25:15 +02:00
6f202363f4
Fixed a typo in doc
Celine Mercier
2017-08-20 17:20:13 +02:00
7f1ff49aa2
Cython API to import a column and a view from a DMS to another DMS
Celine Mercier
2017-08-03 16:34:02 +02:00
4b86aa67a8
New C functions to import a column and a view from a DMS to another DMS
Celine Mercier
2017-08-03 16:33:12 +02:00
a3e81930c2
Views: finished handling and documenting the conditions for an existing column to be added to a view
Celine Mercier
2017-08-03 16:32:22 +02:00
927c684fc2
Utils: new function to copy the content of a file into another file
Celine Mercier
2017-08-03 16:28:54 +02:00
344566d9e9
AVLs: made some functions public and changed some rights to be able to import AVLs from a DMS to another
Celine Mercier
2017-08-03 16:27:43 +02:00
407f61a408
Add the possibility to create temporary objects like a temporary directory and a temporary DMS
Eric Coissac2017-07-28 16:33:19 +02:00
09ddd74652
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
Eric Coissac2017-07-28 15:57:01 +02:00
7c0d882bc9
Patch a bug when creating a DMS not in the current directory. Use the basename function to locate the DMS name instead of the loop...
Eric Coissac2017-07-28 15:56:21 +02:00
35b0c55a8c
Cython API: various improvements and checks
Celine Mercier
2017-07-28 13:15:13 +02:00
0655063bb0
Cython API: view_NUC_SEQS changes to go with previous commits
Celine Mercier
2017-07-27 19:39:26 +02:00
9701b1230c
Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid mismatching method definitions with subclasses
Celine Mercier
2017-07-27 19:38:25 +02:00
1a0f18a11a
Cython API: added a __setitem__ method to the View class that can detect if the item is a Line and create the corresponding columns if needed + minor changes
Celine Mercier
2017-07-27 19:35:28 +02:00
3d7aa52c90
Cython API: Fixed a bug when setting NA values in Column_multi_elts, and added some properties
Celine Mercier
2017-07-27 19:31:15 +02:00
69c50ff922
Cython API: added a Column subclass to allow direct access to indexes for columns that store indexes referring to other data
Celine Mercier
2017-07-27 19:29:10 +02:00
c91969126b
Cython C API declarations to go with previous commit
Celine Mercier
2017-07-27 19:26:59 +02:00
15d383fa8b
Added possibility to specify the offset for encoding and decoding sequence quality character strings
Celine Mercier
2017-07-27 19:24:41 +02:00
99ceed5fff
Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon
Celine Mercier
2017-07-27 19:21:45 +02:00
dc91174a5e
Complete the input option group functions
Eric Coissac2017-07-27 16:06:48 +02:00
ec65f00cf2
Complete the fasta iterator to manage new input options
Eric Coissac2017-07-27 16:05:30 +02:00
8d9cdb4d03
Complete the fastq iterator to manage new input options
Eric Coissac2017-07-27 16:05:17 +02:00
949e5f9baf
Make a first full version of the URI decoder
Eric Coissac2017-07-27 16:04:31 +02:00
3c6a05be54
Add option to the default config corresponding to the parsing of the inputs
Eric Coissac2017-07-27 16:03:47 +02:00
8781ecab1f
Add a factory checking the file format and returning the correct iterator. First version working only with fasta and fastq nucleic formats
Eric Coissac2017-07-27 16:02:52 +02:00
59dd0a8a8c
Standardized and improved the API to create new columns, updated the doc
Celine Mercier
2017-07-18 17:34:32 +02:00
c88df2e12c
First version of automatic ID and COUNT columns, to discuss (for now, columns created when NUC_SEQ views are closed if the columns don't already exist)
Celine Mercier
2017-07-17 17:31:09 +02:00
1e57bfacb4
Fixed some C documentation
Celine Mercier
2017-07-17 16:45:08 +02:00
3e6aecc635
Added a C function to add a COUNT column to a view with all lines set to 1
Celine Mercier
2017-07-11 16:44:23 +02:00
ced9a268a1
obi import: added an option to specify the NA value in the input file (default is 'NA', same as in R's read.table function)
Celine Mercier
2017-07-11 12:10:33 +02:00
df2ad41150
Cython APi: Added a width property to views, corresponding to their column count
Celine Mercier
2017-07-11 11:46:32 +02:00
f8895e879d
Cython API: Added a function to get a column from its index in the view
Celine Mercier
2017-07-11 11:36:42 +02:00
b729b8928f
obi less: fixed bug when the length of a view would be less than the default number of lines printed
Celine Mercier
2017-07-10 17:04:02 +02:00
b6b95f26b6
obi import: Skipping sequences is now done through the iterators so that sequences are not uselessly parsed
Celine Mercier
2017-07-10 17:02:30 +02:00
b94ec9557f
Cython API: None values aren't inclued anymore in the dictionary returned when getting a line from a column with multiple elements per line, and reworked that function to be more optimized
Celine Mercier
2017-07-07 17:28:53 +02:00
143bddf1d1
Cython API: Added an __iter__ method to the class Column_line (iterating on the elements names) (previously an iteration would work but with unexpected results)
Celine Mercier
2017-07-07 15:41:10 +02:00
a718081ebd
Bug with error handling: for now obi_errno needs to be passed to the function handling errors and exceptions, as it can't read the right value of the global obi_errno (Cython configuration problem?)
Celine Mercier
2017-07-07 15:36:11 +02:00
740d021276
obi import: fixed bugs when rewriting a column: a bug with new elements names ignoring previous elements names found, a bug with the global obi_errno being reset too late, and a bug with the column dictionary used by obi import not being updated after rewriting a column
Celine Mercier
2017-07-07 15:33:43 +02:00
906343187b
Fixed bug with view option in obi less and obi check
Celine Mercier
2017-07-06 16:42:27 +02:00
5ee0b3989a
Cython API: set_line of Column_multi_elts now accept as values argument any class where values are referenced by keys with an iterator
Celine Mercier
2017-07-05 17:32:32 +02:00
d10192ab0e
C functions to detect IUPAC sequences
Celine Mercier
2017-07-05 17:26:03 +02:00
101f764cce
New obi import with rewriting of columns when column type or line elements (keys) change
Celine Mercier
2017-07-05 17:15:23 +02:00
cb5ad2ed2d
Added functions to try to open a DMS if it exists
Celine Mercier
2017-07-05 15:38:22 +02:00
f5e992abbf
Added a check on the element when setting a value in a column
Celine Mercier
2017-07-05 14:49:20 +02:00
1d2996c6c0
Better handling and tracing of Index Errors between C and Cython
Celine Mercier
2017-07-05 14:45:43 +02:00
2f0c4b90d7
Fixed a problem where a view would have a wrong line count after adding a first column to it if there was already a Line selection associated (happening when cloning), and fixed a bad error check.
Celine Mercier
2017-04-14 16:25:55 +02:00
537b9847da
Minor C doc clarification
Celine Mercier
2017-04-14 16:23:17 +02:00
b998373be5
Cython API: updated the test command for the new API and deactivated the other commands for now
Celine Mercier
2017-04-14 16:21:33 +02:00
0e08fc486a
Cython API: fixed bug when deleting a column from a view where the Cython wrapper wasn't closed, and fixed the Line selection materialization
Celine Mercier
2017-04-14 16:19:18 +02:00
2bbee64e57
Cython API: fixed problems with Column class
Celine Mercier
2017-04-14 16:14:41 +02:00
693859eec2
Cython API: fixed conversion bugs when setting and getting values (especially NA values) in OBI_CHAR, OBI_STR and OBI_SEQ columns
Celine Mercier
2017-04-14 16:07:23 +02:00
Celine Mercier
Eric Coissac