Commit 38756b55 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-t/3944-pouvoir-calculer-des-distributions-2' into 'dev'

Feature t/3944 pouvoir calculer des distributions 2

Closes #3944

See merge request !504
parents f7cac1de eea5d6c4
Pipeline #93618 failed with stages
in 18 minutes and 10 seconds
......@@ -3,7 +3,7 @@
"samples" : {
"number" : 1,
"original_names" : [ "/some/file" ] ,
"original_names" : [ "/some/file_1" ] ,
"run_timestamp" : [ "2015-02-19 16:37:06" ] ,
"producer" : [ "vidjil dev 0cf35de (2015-02-17)" ] ,
"log" : [ "Some log" ],
......
......@@ -3,7 +3,7 @@
"samples" : {
"number" : 1,
"original_names" : [ "/some/file" ] ,
"original_names" : [ "/some/file_2" ] ,
"run_timestamp" : [ "2015-02-19 16:37:06" ] ,
"producer" : [ "vidjil dev 0cf35de (2015-02-17)" ] ,
"log" : [ "Some log" ],
......
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### Without distributions computing
!LAUNCH: python3 ../../fuse.py --output fused_with_distrib_step1.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_with_distrib_step1.vidjil
$ Get correct file name in original_names field
1:"/some/file_1"
1:"/some/file_2"
$ should not have distribution if not asked
0:distributions
### With distributions computing
#rm fused.vidjil
!LAUNCH: python3 ../../fuse.py --output fused_with_distrib_step2.vidjil -D ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_with_distrib_step2.vidjil
$ Get correct file name in original_names field and distributions
2:"/some/file_1"
2:"/some/file_2"
$ should have two time 'distributions' (console log + into vidjil file)
2:distributions
$ Axis title should be present 122 times (2*60+1/file)
122:lenCDR3
\ No newline at end of file
#######################################
### Part without clones (--no-clone) ##
#######################################
!LAUNCH: python3 ../../fuse.py --no-clones --output fused_without_clones.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_without_clones.vidjil
$ Should not have field clones
0:"clones": \[
###################################
### Part with unsegmented clones ##
###################################
!LAUNCH: python3 ../../fuse.py -D --no-clones --output fused_with_unsegmented_clones_and_complete_distributions.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_with_unsegmented_clones_and_complete_distributions.vidjil
$ Get correct keys for distributions json content
1:"repertoires"
1:"keys"
1:"filters"
$ Get correct files names
r:/some/file_[12]
$ Correct number of entries for some keys (2*30 + 1 by repertoire)
122:"seg5"
122:"lenCDR3"
############################
### Part with real clones ##
############################
!LAUNCH: python3 ../../fuse.py -d germline,seg5 --no-clones --output fused_with_real_clones_and_complete_distributions.vidjil ../../../algo/tests/data/results_five_segmented_clones.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_with_real_clones_and_complete_distributions.vidjil
$ Get correct keys for distributions json content
1:"repertoires"
1:"keys"
1:"filters"
$ No clones
0:"id"
$ Correct number of entries for some keys (1 by repertoire)
3:"seg5"
$ Get correct files names
:sequence_file
$ Filenames (original_files and repname)
2:"sequence_file"
2:"/some/file_1"
2:"/some/file_2"
$ Case of an entire result (axes: germline, seg5)
lr1:"values": { "IGK": { .* "IGKV3-20\*01": \[ 1, 3898 \]
lr1:"values": { "IGK": { .* "IGKV1-39\*01": \[ 1, 5653 \]
lr1:"values": { "IGK": { .* "IGKV1-33\*01": \[ 1, 2597 \]
lr1:"values": { "IGK": { .* "IGKV4-1\*01": \[ 1, 2520 \]
lr1:"values": { "IGK": { .* "IGKV3-15\*01": \[ 1, 2502 \]
$ Case for the two other files (axes: germline, seg5)
lr1:"values": { "IGH": { "\?": \[ 2, 900 \]
lr1:"values": { "IGH": { "\?": \[ 2, 350 \]
####################################################
### Part with real clones, only some distribution ##
####################################################
!LAUNCH: python3 ../../fuse.py -d seg5,seg3 -d evalue -d unknow_AXIS --no-clones --output fused_only_some_axes.vidjil ../../../algo/tests/data/results_five_segmented_clones.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil; cat fused_only_some_axes.vidjil
$ Get correct keys for distributions json content
1:"repertoires"
1:"keys"
1:"filters"
$ No clones
0:"id"
$ Correct number of entries for some keys (1 by repertoire): seg5
3:"seg5"
$ Correct number of entries for some keys (1 by repertoire): unknow_AXIS (axis name)
3:"unknow_AXIS"
$ Correct number of entries for some keys (1 by repertoire): unknow_axis (axis returned value)
3:"unknow_axis"
$ Get correct files names
:sequence_file
$ Filenames (original_files and repname)
2:"sequence_file"
2:"/some/file_1"
2:"/some/file_2"
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