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
f6631f3857
Removed deprecated declarations
2017-07-05 14:42:21 +02:00
3f5fef10b9
obi test: minor changes
2017-07-05 14:37:27 +02:00
20c72af697
Basic obi check command to check DMS and view informations
2017-07-05 13:54:19 +02:00
d252131950
Basic obi less command
2017-07-05 13:44:12 +02:00
ca16ce0bb0
Basic obi grep with new Cython API
2017-07-05 11:58:10 +02:00
ac94b35336
Removed unused import
2017-07-05 11:52:31 +02:00
2d65db4ebc
Goes with c2af955b : forgotten files for NUC_SEQS views
2017-04-21 15:15:12 +02:00
4b037ae236
Updated obi test to test NUC_SEQS views and the taxonomy API
2017-04-21 12:09:04 +02:00
c2af955b78
Cython view API: added NUC_SEQS views and sequence classes + changed
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cloning API
2017-04-21 12:08:14 +02:00
71b1a43df8
Added functions to clone views with a simpler API
2017-04-21 11:58:15 +02:00
1725b8b80c
Reworked taxonomy Cython API to be a subclass of OBIWrapper
2017-04-21 11:54:05 +02:00
ab0d08293e
Cython API: removed unnecessary imports
2017-04-21 11:51:05 +02:00
2f0c4b90d7
Fixed a problem where a view would have a wrong line count after adding
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a first column to it if there was already a Line selection associated
(happening when cloning), and fixed a bad error check.
2017-04-14 16:25:55 +02:00
