c5f3fdc295
Increased maximum element names length in columns
2017-07-27 19:44:49 +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
59dd0a8a8c
Standardized and improved the API to create new columns, updated the doc
2017-07-18 17:34:32 +02:00
c88df2e12c
First version of automatic ID and COUNT columns, to discuss (for now,
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columns created when NUC_SEQ views are closed if the columns don't
already exist)
2017-07-17 17:31:09 +02:00
1e57bfacb4
Fixed some C documentation
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
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1
2017-07-11 16:44:23 +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
f03928c679
Committing minor comments before merging branch with master
2017-07-06 10:56:39 +02:00
717ee46f08
Commented a loose print
2017-07-05 18:02:18 +02:00
313508cc94
Better *Seq* classes but still need work
2017-07-05 17:53:46 +02:00
535fc2af83
Column rewriter and optimized View getter
2017-07-05 17:49:05 +02:00
3bbc2ae469
More optimized Column item getter
2017-07-05 17:37:19 +02:00
5ee0b3989a
Cython API: set_line of Column_multi_elts now accept as values argument
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any class where values are referenced by keys with an iterator
2017-07-05 17:32:32 +02:00
d10192ab0e
C functions to detect IUPAC sequences
2017-07-05 17:26:03 +02:00
101f764cce
New obi import with rewriting of columns when column type or line
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elements (keys) change
2017-07-05 17:15:23 +02:00
cb5ad2ed2d
Added functions to try to open a DMS if it exists
2017-07-05 15:38:22 +02:00
f5e992abbf
Added a check on the element when setting a value in a column
2017-07-05 14:49:20 +02:00
1d2996c6c0
Better handling and tracing of Index Errors between C and Cython
2017-07-05 14:45:43 +02:00
