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v3.0.1b10
obitools3/python/obitools3/commands
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mercierc 3e45c34491 import: now imports and adds taxids for SILVA and RDP files, added 
import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option
2021-06-01 09:21:07 +12:00
..
__init__.py
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
.gitignore
Cleaning first stage
2019-03-29 16:40:36 +01:00
addtaxids.pyx
typo fix
2021-06-01 09:09:16 +12:00
align.pxd
better cfiles
2019-02-19 14:11:29 +01:00
align.pyx
align: fixed column URI parsing
2021-06-01 09:10:21 +12:00
alignpairedend.pxd
Alignpairedend: added alignment using shifting with best kmer similarity
2019-01-21 17:30:46 +01:00
alignpairedend.pyx
small doc fixes
2021-03-29 13:07:48 +13:00
annotate.pyx
Python: made all commands handle output to buffer object (e.g. stdout)
2020-07-24 16:09:48 +02:00
build_ref_db.pyx
build_ref_db: set default threshold to 0.99
2021-06-01 09:11:17 +12:00
cat.pyx
cat: fixed the handling of dictionary columns
2021-06-01 09:06:13 +12:00
clean_dms.pyx
clean_dms: now works with extension
2019-12-12 17:02:50 +01:00
clean.pyx
clean: hid not implemented option
2021-06-01 09:04:22 +12:00
count.pyx
count: added option to specify the count column
2021-06-01 09:05:14 +12:00
ecopcr.pyx
Python: made all commands handle output to buffer object (e.g. stdout)
2020-07-24 16:09:48 +02:00
ecotag.pyx
ecotag: clarified similarity circle documentation
2020-09-29 17:57:29 +02:00
export.pyx
export: now automatically sorts dictionary keys alphabetically for
2020-07-31 16:43:35 +02:00
grep.pyx
grep: added taxonomy check
2021-05-31 17:03:39 +12:00
head.pyx
small doc fixes
2021-03-29 13:07:48 +13:00
history.pyx
all commands (almost): cleaner DMS closing at the end
2020-04-12 17:31:58 +02:00
import.pyx
import: now imports and adds taxids for SILVA and RDP files, added
2021-06-01 09:21:07 +12:00
less.pyx
all commands (almost): cleaner DMS closing at the end
2020-04-12 17:31:58 +02:00
ls.pyx
obi ls: now done in C (preparing things for R packages to read DMS) and
2020-09-29 17:51:39 +02:00
ngsfilter.pyx
small fixes
2021-04-07 10:28:02 +12:00
rm.pyx
new command: obi rm: deletes any view (for now the user deleting a view
2021-03-18 09:17:06 +13:00
sort.pyx
small doc fixes
2021-03-29 13:07:48 +13:00
stats.pyx
obi stats: various fixes and improvements
2021-05-31 16:51:06 +12:00
tail.pyx
small doc fixes
2021-03-29 13:07:48 +13:00
test.pyx
small doc fixes
2021-03-29 13:07:48 +13:00
uniq.pxd
obi uniq: fixed the remerging of already merged informations, and
2020-05-07 17:05:54 +02:00
uniq.pyx
uniq: now OK to use -m option even if only one unique key in information
2021-03-15 16:48:22 +13:00