73bca6288f
New obi uniq
2017-08-20 18:04:21 +02:00
6a2759eee6
obi import with new input/ouput API
2017-08-20 17:58:36 +02:00
663a1a1091
Cython API: column elements: added possibility to check if an element
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exists from its index, and a dict-like get() method
2017-08-20 17:44:05 +02:00
c6d5436a58
Cython API: fixed a bug where iteration on a NUC_SEQS view would not be
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done correctly (bug appeared with optimization modifications done
lately)
2017-08-20 17:41:41 +02:00
47cad285d6
Cython API: fixed 2 little bugs in Seq API
2017-08-20 17:39:30 +02:00
74f15d1a23
Cython API: Various fixes in input handlers (parsers, openers etc).
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Mostly working but not bug-free
2017-08-20 17:37:51 +02:00
7f1ff49aa2
Cython API to import a column and a view from a DMS to another DMS
2017-08-03 16:34:02 +02:00
407f61a408
Add the possibility to create temporary objects like a temporary
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directory and a temporary DMS
2017-07-28 16:33:19 +02:00
35b0c55a8c
Cython API: various improvements and checks
2017-07-28 13:15:13 +02:00
b9c65a871f
Patch decoding of URL
2017-07-28 12:41:28 +02:00
84bb93096f
Cython API: fixes and improvements in Column API
2017-07-28 10:27:04 +02:00
01c69e7e25
Cython API: fixed a bug when printing a column
2017-07-28 10:01:56 +02:00
adf5cbef97
Added DMS method to create a DMS if it doesn't already exists, otherwise
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opens it
2017-07-28 09:55:43 +02:00
da48a9d1af
Patch group of option : types must be callable not a string
2017-07-28 09:36:18 +02:00
9482c663c0
minor comments and changes
2017-07-27 19:46:34 +02:00
89e2f80fd8
Goes with previous commit
2017-07-27 19:43:00 +02:00
7112f44fb7
Bug fixes for input handlers, openers, parsers etc. Compiling but not
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tested
2017-07-27 19:42:44 +02:00
b2fc1f4611
obi uniq: first version
2017-07-27 19:40:19 +02:00
75f691d55a
Cython API: Seq classes reworked
2017-07-27 19:39:58 +02:00
0655063bb0
Cython API: view_NUC_SEQS changes to go with previous commits
2017-07-27 19:39:26 +02:00
9701b1230c
Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid
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mismatching method definitions with subclasses
2017-07-27 19:38:25 +02:00
f8a4428674
Cython API: DMS test_open method doesn't raise an exception anymore
2017-07-27 19:36:28 +02:00
1a0f18a11a
Cython API: added a __setitem__ method to the View class that can detect
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if the item is a Line and create the corresponding columns if needed +
minor changes
2017-07-27 19:35:28 +02:00
3d7aa52c90
Cython API: Fixed a bug when setting NA values in Column_multi_elts, and
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added some properties
2017-07-27 19:31:15 +02:00
69c50ff922
Cython API: added a Column subclass to allow direct access to indexes
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for columns that store indexes referring to other data
2017-07-27 19:29:10 +02:00
c91969126b
Cython C API declarations to go with previous commit
2017-07-27 19:26:59 +02:00
15d383fa8b
Added possibility to specify the offset for encoding and decoding
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sequence quality character strings
2017-07-27 19:24:41 +02:00
99ceed5fff
Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon
2017-07-27 19:21:45 +02:00
fa8f826cdc
Cleanup the end of the file
2017-07-27 16:07:39 +02:00
dc91174a5e
Complete the input option group functions
2017-07-27 16:06:48 +02:00
ec65f00cf2
Complete the fasta iterator to manage new input options
2017-07-27 16:05:30 +02:00
8d9cdb4d03
Complete the fastq iterator to manage new input options
2017-07-27 16:05:17 +02:00
949e5f9baf
Make a first full version of the URI decoder
2017-07-27 16:04:31 +02:00
3c6a05be54
Add option to the default config corresponding to the parsing of the
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inputs
2017-07-27 16:03:47 +02:00
8781ecab1f
Add a factory checking the file format and returning the correct
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iterator. First version working only with fasta and fastq nucleic
formats
2017-07-27 16:02:52 +02:00
0f6ae7dfa6
Options stuff... ;-)
2017-07-25 13:07:03 +02:00
28259cd88b
Beginning of URI decoder -- !!! NOT YET FULLY IMPLEMENTED !!!
2017-07-25 13:05:58 +02:00
b24be84b0a
Add a first group of options
2017-07-25 11:14:30 +02:00
ced9a268a1
obi import: added an option to specify the NA value in the input file
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(default is 'NA', same as in R's read.table function)
2017-07-11 12:10:33 +02:00
df2ad41150
Cython APi: Added a width property to views, corresponding to their
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column count
2017-07-11 11:46:32 +02:00
f8895e879d
Cython API: Added a function to get a column from its index in the view
2017-07-11 11:36:42 +02:00
b729b8928f
obi less: fixed bug when the length of a view would be less than the
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default number of lines printed
2017-07-10 17:04:02 +02:00
b6b95f26b6
obi import: Skipping sequences is now done through the iterators so that
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sequences are not uselessly parsed
2017-07-10 17:02:30 +02:00
b94ec9557f
Cython API: None values aren't inclued anymore in the dictionary
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returned when getting a line from a column with multiple elements per
line, and reworked that function to be more optimized
2017-07-07 17:28:53 +02:00
143bddf1d1
Cython API: Added an __iter__ method to the class Column_line (iterating
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on the elements names) (previously an iteration would work but with
unexpected results)
2017-07-07 15:41:10 +02:00
a718081ebd
Bug with error handling: for now obi_errno needs to be passed to the
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function handling errors and exceptions, as it can't read the right
value of the global obi_errno (Cython configuration problem?)
2017-07-07 15:36:11 +02:00
740d021276
obi import: fixed bugs when rewriting a column: a bug with new elements
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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
2017-07-07 15:33:43 +02:00
906343187b
Fixed bug with view option in obi less and obi check
2017-07-06 16:42:27 +02:00
c3cd57a9e3
Removed deprecated file
2017-07-06 10:57:14 +02:00
717ee46f08
Commented a loose print
2017-07-05 18:02:18 +02:00
