Commit 96ae781e authored by flothoni's avatar flothoni

Add test on loading a vidjil file without clone inside (option --no-clone for example)

Link to #4172
parent 40034e51
Pipeline #119181 passed with stages
in 7 minutes and 50 seconds
# coding: utf-8
load 'vidjil_browser.rb'
load 'browser_test.rb'
#browser test suite
class TestClones < BrowserTest
def setup
super
if not defined? $b
set_browser("/demo/Demo-X5-no-clone.vidjil")
if $b.div(id: 'tip-container').present?
$b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
end
# Make upload menu appear to test the application with this menu too
$b.execute_script("$('#upload_summary')[0].style.display='block';")
end
end
def after_tests
end
##############
### CLONES ###
##############
# no clone present in this file, but only log, reads numbers, ...
def test_000_clone_present_inlist
info = $b.div(:id => "info_segmented")
assert ( info.title == "total: 14" )
assert ( not $b.clone_in_list('0').exists?), ">> No clone exist in list"
end
# Not really a test
def test_zz_close
close_everything
end
end
{
"clones": null,
"config": {
"all": false,
"alternative-genes": "0",
"analysis-e-value-D": "0.05",
"analysis-filter": "1",
"cdr3": false,
"clean-memory": false,
"cluster-N": "10",
"cluster-epsilon": "0",
"cluster-load-matrix": false,
"cluster-save-matrix": false,
"consensus-on-longest-sequences": false,
"dir": "./out/",
"e-value": "1",
"e-value-kmer": "-1",
"germline": "germline/homo-sapiens.g",
"help-advanced": false,
"label-filter": false,
"max-consensus": "100",
"min-ratio": "0",
"min-reads": "5",
"no-airr": false,
"no-vidjil": false,
"not-analyzed-as-clones": false,
"out-affects": false,
"out-analyzed": false,
"out-reads": false,
"out-unanalyzed": false,
"plain-index": false,
"several-D": false,
"verbose": false
},
"diversity": {
"index_Ds_diversity": 1.0,
"index_E_equitability": 1.0000001192092896,
"index_H_entropy": 2.639057606458664
},
"germlines": {
"custom": {
"3": [],
"4": [],
"5": [],
"shortcut": "X"
},
"ref": "http://www.vidjil.org/germlines/germline-59.tar.gz",
"species": "Homo sapiens",
"species_taxon_id": 9606
},
"reads": {
"germline": {
"IGH": [
1
],
"IGH+": [
1
],
"IGK": [
1
],
"IGK+": [
2
],
"IGL": [
1
],
"TRA": [
1
],
"TRA+D": [
1
],
"TRB": [
1
],
"TRB+": [
1
],
"TRD": [
1
],
"TRD+": [
2
],
"TRG": [
1
]
},
"segmented": [
14
],
"total": [
14
]
},
"samples": {
"commandline": [
"./vidjil-algo -g germline/homo-sapiens.g demo/Demo-X5.fa "
],
"log": [
" ==> junction detected in 14 reads (100%)\n ==> found 14 windows in 14 reads (100% of 14 reads)\n reads av. len clones clo/rds\n IGH -> 1 353.0 1 1.000\n IGH+ -> 1 182.0 1 1.000\n IGK -> 1 372.0 1 1.000\n IGK+ -> 2 280.5 2 1.000\n IGL -> 1 327.0 1 1.000\n TRA -> 1 155.0 1 1.000\n TRA+D -> 1 420.0 1 1.000\n TRB -> 1 177.0 1 1.000\n TRB+ -> 1 152.0 1 1.000\n TRD -> 1 194.0 1 1.000\n TRD+ -> 2 204.0 2 1.000\n TRG -> 1 115.0 1 1.000\n\n SEG -> 14 244.0\n SEG_+ -> 14 244.0\n SEG_- -> 0 -\n SEG changed w -> 0 -\n\n UNSEG too short -> 0 -\n UNSEG strand -> 0 -\n UNSEG too few V/J -> 0 -\n UNSEG only V/5' -> 0 -\n UNSEG only J/3' -> 0 -\n UNSEG < delta_min -> 0 -\n UNSEG ambiguous -> 0 -\n UNSEG too short w -> 0 -\n"
],
"number": 1,
"original_names": [
"demo/Demo-X5.fa"
],
"producer": [
"vidjil-algo dev 40034e517 (2020-02-03)"
],
"run_timestamp": [
"2020-02-03 16:29:22"
]
},
"vidjil_json_version": "2016b"
}
\ No newline at end of file
locus duplicate_count v_call d_call j_call sequence_id sequence productive junction_aa junction cdr3_aa warnings rev_comp sequence_alignment germline_alignment v_cigar d_cigar j_cigar
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