Commits · e7cca3181bbdfcd65874cfbbffef7dd216fc4c2a · vidjil / vidjil

20 Nov, 2020 2 commits
- fuse.py; add a function addWarning · 5ada8528
  flothoni authored Nov 20, 2020
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Link to 4566
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  5ada8528
- fuse & warning, add a new warning if clone have not same name between samples · 31b2bd64
  flothoni authored Nov 20, 2020
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Link to #4566
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  31b2bd64
16 Sep, 2020 1 commit

fuse.py; Allow to add option for preprocess script execution · ee5a9e74

flothoni authored Sep 16, 2020

Now, preprocess can have more option by this modification
BUT preprocess script should also take -i/-o args for execution

ee5a9e74

07 Aug, 2020 2 commits
- fuse.py, remove useless string · 3f5b53c4
  flothoni authored Aug 07, 2020
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Link to #3830
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  3f5b53c4
- fuse; update overlaps index testing · dc031da7
  flothoni authored Aug 07, 2020
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Link to #3830
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  dc031da7
04 Aug, 2020 1 commit
- fuse.py & test; Overlap is calculated if options is set · 12472d30
  flothoni authored Aug 04, 2020
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Update test to use this new parameter
Update test to use json values
Link to #3830"
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  12472d30
28 Jul, 2020 1 commit
- Morisita index; update function from fuse. · 4f23358a
  flothoni authored Jul 28, 2020
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* update tests
* Move results into 'overlaps' key in vidjil export
Link to #3830
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  4f23358a
08 Jul, 2020 1 commit
- update Morisita index computation from fuse script · 5e21a7e6
  flothoni authored Jul 09, 2020
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Link to #3830
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  5e21a7e6
21 Apr, 2020 1 commit
- fuse.py: opens .gz files · fac94da4
  Mathieu Giraud authored Apr 21, 2020
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Closes #4254
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  fac94da4
20 Mar, 2020 1 commit
- fuse; update test after fuse correction on top · 730a0ce4
  flothoni authored Mar 20, 2020
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Link to #4199
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  730a0ce4
12 Mar, 2020 1 commit
- fuse.py; add ratio_semgented column for airr export · f0a63559
  flothoni authored Mar 12, 2020
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Link to #4199
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  f0a63559
10 Mar, 2020 1 commit
- fuse.py; update cut limit · 0740a0e5
  Thonier Florian authored Mar 10, 2020
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Link to #4213
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  0740a0e5
04 Mar, 2020 1 commit
- fuse.py; change content of constante GET_UNKONW_AXIS · dcb9eedb
  flothoni authored Mar 04, 2020
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Link to #4199
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  dcb9eedb
03 Mar, 2020 6 commits
- fuse.py; replace string for unknow_axis result · b01e3678
  flothoni authored Mar 03, 2020
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Link to #4199
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  b01e3678
- fuse.py; add option to export into AIRR format · 2b0abe8c
  flothoni authored Mar 03, 2020
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each clone will be added in one line, and multiple time if present in multiple sample
each line will have the filename field of the clone, and also the ratio of the clone and the his locus
Link to #4199
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  2b0abe8c
- tools; update tests on export to airr format · 9797b8c3
  flothoni authored Mar 03, 2020
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Link to #4199
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  9797b8c3
- fuse.py; update export airr function · c8f896fd
  flothoni authored Mar 03, 2020
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link to #4199
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  c8f896fd
- fuse.py: update some axis for airr export · b6934f22
  flothoni authored Mar 03, 2020
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Link to #4199
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  b6934f22
- fuse.py; remove airr columns not available for export · 86601740
  flothoni authored Mar 03, 2020
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Link to #4199
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  86601740
25 Feb, 2020 1 commit
- fuse.py; export AIRR; add a try/except loop for non constant keys · f7302948
  flothoni authored Feb 25, 2020
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Link to #4199
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  f7302948
24 Feb, 2020 4 commits
- fuse.py; add an option to make an export in AIRR format in the main call · 4d347ea8
  flothoni authored Feb 24, 2020
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Link to #4199
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  4d347ea8
- fuse.py; add an export function into Jlist object · c1465b89
  flothoni authored Feb 24, 2020
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Make a line for each time that a clone is present (with filename added)
Link to #4199
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  c1465b89
- fuse.py; Add an function to get clone as a csv line ready to export · 35506409
  flothoni authored Feb 24, 2020
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Take a list of columns to export, a timepoint, and the associated jlist object in parameter
Link to #4199
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  35506409
- fuse.py; add some axis available by windows get_values function · 75a63ac3
  flothoni authored Feb 24, 2020
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Link to #4199
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  75a63ac3
21 Jan, 2020 14 commits
- fuse.py; now, airr value are converted (int, bool) if needed · f3b53f37
  flothoni authored Jan 17, 2020
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Some software don't give correct bool value and should be converted
Link to #3673
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  f3b53f37
- fuse.py; minor change in comments · 56f7c89a
  flothoni authored Jan 14, 2020
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Link to #3673
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  56f7c89a
- fuse.py: some comments · f2b05710
  Mathieu Giraud authored Jan 14, 2020
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together with @flothoni
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  f2b05710
- fuse.py; remove bypass on unsegmented row and add cdr1 for exemple · 3a47872b
  flothoni authored Dec 18, 2019
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CDR1 value are given in imgt files and have a start/stop couple of data. This is translate in the vidjil file
Link to #3673
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  3a47872b
- fuse; AIRR import; give an undefined values if no germline given · 0fd472a7
  flothoni authored Dec 16, 2019
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Link to #3673
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  0fd472a7
- fuse; AIRR import; add warnings usage (as define by vidjil) · ab6e080e
  flothoni authored Dec 16, 2019
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Link to #3673
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  ab6e080e
- fuse; AIRR import; minor bug fix · 50802d71
  flothoni authored Dec 16, 2019
  
  50802d71
- fuse; AIRR import; better naming · 2c4e10e0
  flothoni authored Dec 16, 2019
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Link to #3673
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  2c4e10e0
- fuse.py; AIRR import; add cleaning step to erase supplmentary data · a013beff
  flothoni authored Dec 16, 2019
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Link to #3673
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  a013beff
- fuse.p, AIRR import; add control on id of clone to avoid duplicate · 4d130682
  flothoni authored Dec 16, 2019
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Link to #3673
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  4d130682
- fuse.py, function load_airr; don't add empty values · 3818fd17
  flothoni authored Dec 10, 2019
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If a clone have no value for a column, don't add an empty value in clone data; Link to #3673
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  3818fd17
- fuse.py; refactor function load_airr · d379b7c3
  flothoni authored Dec 10, 2019
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Now each axe have it own declaration and is tested for presence or not inside the loaded airr file
Link to #3673
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  d379b7c3
- fuse.py; add airr axes name as use by mixcr · b5278b2e
  flothoni authored Dec 10, 2019
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mixcr don't use airr column names. So we need to make correlation between their names and airr names
Link to #3673
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  b5278b2e
- fuse.py; add function to use AIRR formated files. · 0b574ffe
  flothoni authored Dec 05, 2019
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Link to #3673
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  0b574ffe
26 Sep, 2019 2 commits
- fuse.py; move a call to distributions at the jlist loading · 588a503d
  flothoni authored Sep 26, 2019
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Allow to create distribution before cut of non top clones
Link to #3978
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  588a503d
- fuse.py; add a function to round some axes if needed · bab8df68
  flothoni authored Sep 26, 2019
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Update some doctest
Link to #3978
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  bab8df68