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Author SHA1 Message Date
Celine Mercier 8f1d94fd24 obi test: fixed bug introduced in ad1fd3c3 2021-03-11 16:31:31 +13:00
Celine Mercier 41fbae7b6c Switch to version 3.0.0b43 2021-03-10 16:52:03 +13:00
Celine Mercier ad1fd3c341 Now handling dictionaries with one key 2021-03-10 16:50:30 +13:00
Celine Mercier fbf0f7dfb6 import: improved genbank parser and switch to version 3.0.0b42 2021-02-17 15:26:35 +13:00
Celine Mercier fda0edd0d8 Switch to version 3.0.0b41 2021-02-10 17:29:08 +13:00
Celine Mercier 382e37a6ae Fixes #88 2021-02-10 17:28:49 +13:00
Celine Mercier 5cc3e29f75 obi test: made less heavy by default 2021-02-10 17:28:15 +13:00
Celine Mercier a8e2aee281 Switch to version 3.0.0b40 2021-02-06 14:45:07 +13:00
Celine Mercier 8ba7acdfe1 export: fixed a bug where exporting to tab format with a header would 
not export the first line of data and switch to version 3.0.0b39
 2021-01-13 16:09:04 +01:00
Celine Mercier 38051b1e4f Removed spurious commentaries 2021-01-13 16:07:42 +01:00
Celine Mercier 52a2e21b38 grep: fixed --id-list option 
and switch to version 3.0.0b38
 2020-11-06 16:36:37 +01:00
Celine Mercier d27a5b9115 Switch to version 3.0.0b37 2020-10-30 10:47:13 +01:00
Celine Mercier 20bd3350b4 New command: obi addtaxids to add NCBI taxids to sequences from their 
taxon name.
 2020-10-30 10:46:55 +01:00
Celine Mercier 2e191372d7 Now handling sequences with Uracil (U) nucleotides by converting to 
Thymine (T)
 2020-10-30 10:46:17 +01:00
Celine Mercier 112e12cab0 Taxonomy: new functions to find taxa by name 2020-10-30 10:45:20 +01:00
Celine Mercier b9b4cec5b5 import: now can import SILVA fasta files 2020-10-30 10:43:04 +01:00
Celine Mercier 199f3772e8 Small fixes (potential compilation problems) 2020-10-30 10:41:58 +01:00
Celine Mercier 422a6450fa ecotag: clarified similarity circle documentation 2020-09-29 17:57:29 +02:00
Celine Mercier 137c109f86 obi ls: now done in C (preparing things for R packages to read DMS) and 
switch to version 3.0.0b36
 2020-09-29 17:51:39 +02:00
Celine Mercier b6648ae81e Revert "Fixed version numbering mistake (should be b34 not b35)" 
This reverts commit f6dffbecfe
 2020-09-25 16:25:39 +02:00
Celine Mercier f6dffbecfe Fixed version numbering mistake (should be b34 not b35) 2020-09-25 16:24:23 +02:00
Celine Mercier c4696ac865 ecotag: added separate threshold for minimum circle identity (and switch 
to version 3.0.0b35
 2020-09-25 16:22:09 +02:00
Celine Mercier 11a0945a9b obi cat: fixed open file descriptor leak and switch to version 3.0.0b34 2020-08-28 10:41:22 +02:00
Celine Mercier f23c40c905 obi cat: fixed a bug introduced in 3.0.0b28 and switch to version 
3.0.0b33
 2020-08-27 18:38:16 +02:00
Celine Mercier f99fc13b75 switch to version 3.0.0b32 2020-08-13 18:17:09 +02:00
Celine Mercier 1da6aac1b8 C: patch for failed creation of AVL with errno EEXIST 2020-08-12 17:55:08 +02:00
Celine Mercier 159803b40a export: now automatically sorts dictionary keys alphabetically for 
tab/csv output
 2020-07-31 16:43:35 +02:00
Celine Mercier 7dcbc34017 import: fixed entry count estimation when importing fastq files 2020-07-30 16:56:36 +02:00
Celine Mercier db2202c8b4 uniq: added a check to make sure that there is more than one element for 
one tag when merging its information
 2020-07-30 16:14:37 +02:00
Celine Mercier d33ff97846 switch to version 3.0.0b31 2020-07-28 09:31:19 +02:00
Celine Mercier 1dcdf69f1f export: fixed a bug introduced in version 3.0.0b28 2020-07-28 09:31:05 +02:00
Celine Mercier dec114eed6 Python: added "date created" information in view representation 2020-07-27 17:38:45 +02:00
Celine Mercier f36691053b Python: added the OBITools3 version that generated the view in view 
comments
 2020-07-27 16:50:00 +02:00
Celine Mercier f2aa5fcf8b alignpairedend: fixed division by 0 bug and switch to version 3.0.0b30 2020-07-27 10:15:59 +02:00
Celine Mercier bccb3e6874 switch to version 3.0.0b29 2020-07-26 17:40:26 +02:00
Celine Mercier f5a17bea68 C: added a missing error check 2020-07-26 17:39:55 +02:00
Celine Mercier e28507639a C and Cython: fixed and improved the associated columns system 2020-07-26 17:39:29 +02:00
Celine Mercier e6feac93fe obi test: made less heavy to be faster 2020-07-26 17:37:21 +02:00
Celine Mercier 50b292b489 obi import: added --space-priority option to import a view line by line 2020-07-26 17:36:52 +02:00
Celine Mercier 24a737aa55 switch to version 3.0.0b28 2020-07-24 16:10:10 +02:00
Celine Mercier 8aa455ad8a Python: made all commands handle output to buffer object (e.g. stdout) 2020-07-24 16:09:48 +02:00
Celine Mercier 46ca693ca9 Cython: View: new method to print a view to a buffer (e.g. stdout) 2020-07-24 16:03:23 +02:00
Celine Mercier 9a9afde113 Cython: progress bar: set default refresh rate to 5 seconds 2020-07-24 15:29:12 +02:00
Celine Mercier 8dd403a118 grep: now prints the number of entries grepped 2020-07-13 17:08:13 +02:00
Celine Mercier 9672f01c6a alignpairedend: improved/fixed the output tags for the alignment score 
and lengths. Removed minimum score option
 2020-07-13 15:59:50 +02:00
Celine Mercier ed9549acfb ngsfilter: unidentified sequences are now stored untrimmed 2020-07-13 15:56:40 +02:00
Celine Mercier 9ace9989c4 Switch to version 3.0.0b27 2020-07-07 16:47:21 +02:00
Celine Mercier a3ebe5f118 C: AVL trees: fixed a bug where storing the difference between 2 crc64 
values in an int64 would mess trees up resulting in failed data
dereplication
 2020-07-07 16:47:00 +02:00
Celine Mercier 9100e14899 obi uniq: quick fix for bug where some sequences are not correctly 
dereplicated
 2020-07-03 17:36:57 +02:00
Celine Mercier ccda0661ce small help documentation improvement 2020-07-01 18:20:38 +02:00
Celine Mercier aab59f2214 obi clean: fixed a memory bug, fixed the behaviour when no sample info, 
and added checks warnings and error handling when sample info not
dereplicated
 2020-07-01 18:17:47 +02:00
Celine Mercier ade1107b42 switch to version 3.0.0b26 2020-06-17 18:56:07 +02:00
Celine Mercier 9c7d24406f export: dictionaries are now formatted like in the original OBITools 
when exporting in tabular format and tuple formatting is cleaner
 2020-06-17 18:55:46 +02:00
Celine Mercier 03bc9915f2 Cython: utils: added handling of tuples to bytes2str_object function 2020-06-17 18:54:14 +02:00
Celine Mercier 24b1dab573 Cython: Columns: added a keys() method that returns all element names 2020-06-17 18:53:41 +02:00
Celine Mercier 7593673f3f ngsfilter: now setting 'reversed' tag to False instead of None when 
false
 2020-06-17 18:52:35 +02:00
Celine Mercier aa01236cae switch to version 3.0.0b25 2020-06-13 21:48:49 +02:00
Celine Mercier 49b8810a76 C: made indexer opening/closing cleaner 2020-06-13 21:47:03 +02:00
Celine Mercier 7a39df54c0 ls: fixed an issue where big DMS couldn't be read by ls 2020-06-13 21:45:22 +02:00
Celine Mercier 09e483b0d6 switch to temporary version 3.0.0b24a 2020-06-10 17:47:56 +02:00
Celine Mercier 14a2579173 uniq: now outputs an empty view if input view is empty instead of 
displaying an error
 2020-06-10 17:47:26 +02:00
Celine Mercier 36a8aaa92e grep: now creating empty views instead of displaying an error when 
selecting on an unexisting column/tag
 2020-06-10 16:57:42 +02:00
Celine Mercier a17eb445c2 ngsfilter: made one of the tag error messages more accurate 2020-06-10 16:27:36 +02:00
Celine Mercier e4a32788c2 Switch to version 3.0.0b24 2020-06-09 14:36:58 +02:00
Celine Mercier 2442cc80bf Cython: View: fixed bash history display 2020-06-09 14:36:37 +02:00
Celine Mercier aa836b2ace uniq: improved progress bar of second browsing 2020-06-09 14:36:02 +02:00
Celine Mercier 8776ce22e6 C: fixed a bug where indexers referring to tuples of certain types were 
not properly closed and imported
 2020-06-09 14:34:43 +02:00
Celine Mercier 4aa772c405 ecotag: Added list of taxids for all best matches (closes #80) 2020-06-09 14:33:14 +02:00
Celine Mercier b0b96ac37a version 3.0.0b23a 2020-06-05 16:10:24 +02:00
Celine Mercier 687e42ad22 C: kmer alignment: fixed a bug where scores of 0 were at 
(0+kmer_length-1) (and now setting alignment direction to None if score
is 0
 2020-06-05 16:09:33 +02:00
Celine Mercier 5fbbb6d304 alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences 
where only the forward sequence was kept
 2020-06-05 16:06:43 +02:00
Celine Mercier 359a9fe237 Switch to version 3.0.0b23 2020-06-04 15:35:03 +02:00
Celine Mercier f9b6851f75 Python: correctly flagged some mandatory options as required 2020-06-04 15:34:24 +02:00
Celine Mercier 2a2c233936 obi import: fixed a bug when skipping an entry 2020-05-29 21:19:42 +02:00
Celine Mercier faf8ea9d86 Switch to version 3.0.0b21 2020-05-28 20:42:09 +02:00
Celine Mercier ffe2485e94 Genbank parser: now reading ORIGIN lines with comments without 
triggering error
 2020-05-28 20:41:34 +02:00
Celine Mercier 6094ce2bbc obi import: skip on error more robust 2020-05-28 20:40:36 +02:00
Celine Mercier a7dcf16c06 Minor changes for pip release 2020-05-20 15:59:04 +02:00
Celine Mercier f13f8f6165 obi import: minor doc/display improvements 2020-05-20 11:46:29 +02:00
Celine Mercier b5a29ac413 Switch to version 3.0.0b19 2020-05-20 10:29:36 +02:00
Celine Mercier efd2b9d338 Cleaner installation 2020-05-20 10:29:12 +02:00
Celine Mercier ca6e3e7aad obi import: fixed to work with seq genbank extension 2020-05-20 10:28:14 +02:00
Celine Mercier 76ed8e18e5 Switch to version 3.0.0b18 with version formatting that fits setuptools 2020-05-18 17:08:55 +02:00
Celine Mercier 1d17f28aec setup: now using setuptools instead of distutils to work with pip 2020-05-18 17:08:09 +02:00
Celine Mercier fa834e4b8b obi import: small bug fix 2020-05-18 17:06:58 +02:00
Celine Mercier a72fea3cc9 Python: fasta parser: fixed a bug stopping the program when the last 
line contained a single nucleotide
 2020-05-12 11:24:12 +02:00
Celine Mercier e9a37d8a6e Switch to version 3.0.0-beta16 2020-05-07 17:09:26 +02:00
Celine Mercier ef074f8455 typo 2020-05-07 17:08:59 +02:00
Celine Mercier aec5e69f2c C, views: no more automatic COUNT column if MERGED_sample column exists 2020-05-07 17:08:07 +02:00
Celine Mercier 170ef3f1ba Views: added obi prefix to commands in bash history 2020-05-07 17:07:01 +02:00
Celine Mercier f999946582 obi uniq: fixed the remerging of already merged informations, and 
efficiency improvements
 2020-05-07 17:05:54 +02:00
Celine Mercier 773b36ec37 obi import: fixed the import of old obitools files with premerged 
informations, and other minor improvements
 2020-05-07 17:03:04 +02:00
Celine Mercier 69cb434a6c version 3.0.0-beta15c 2020-04-29 14:25:33 +02:00
Celine Mercier 55d4f98d60 obi annotate: fixed annotation at ranks 2020-04-29 14:24:40 +02:00
Celine Mercier 0bec2631e8 ecotag: fixed a bug where all the full DMS path weren't properly sent to 
the C layer
 2020-04-29 10:35:55 +02:00
Celine Mercier e6b6c6fa84 AVLs: Made an error message more informative 2020-04-29 10:14:04 +02:00
Celine Mercier 974528b2e6 build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest 
similarities)
 2020-04-28 15:56:06 +02:00
Celine Mercier 1b346b54f9 ecotag: better specificity by now correctly looking for similarities 
within refs above best score instead of ecotag threshold
 2020-04-28 15:10:07 +02:00
Celine Mercier 058f2ad8b3 ecopcr: fixed a bug where sequences were considered circular (generating 
false positives)
 2020-04-27 14:44:35 +02:00
Celine Mercier 60bfd3ae8d obi annotate: now defaults to setting str if expression is not valid 2020-04-24 11:35:20 +02:00