Commit 08947610 authored by florian.thonier's avatar florian.thonier

should_get : fuse.py test with vidjil file without clones.

parent e9a88a82
{
"clones": null,
"diversity": {
"index_Ds_diversity": 1,
"index_E_equitability": -0,
"index_H_entropy": 0
},
"germlines": {
"custom": {
"3": [],
"4": [],
"5": [],
"shortcut": "X"
}
},
"reads": {
"germline": {
"IGH": [
0
],
"IGH+": [
0
],
"IGK": [
0
],
"IGK+": [
0
],
"IGL": [
0
],
"TRA": [
0
],
"TRA+D": [
0
],
"TRB": [
0
],
"TRB+": [
0
],
"TRD": [
0
],
"TRD+": [
0
],
"TRG": [
0
]
},
"segmented": [
0
],
"total": [
1
]
},
"samples": {
"commandline": [
"vidjil -w 50 -c clones -y all -z all -d -3 -r 10 -g /home/florian/vidjil/germline -i -e 0.0001 -o . small_V.fa "
],
"log": [
" ==> junction detected in 0 reads (0%)\n ==> found 0 50-windows in 0 reads (0% of 1 reads)\n ! There are not so many CDR3 windows found in this set of reads.\n ! Please check the unsegmentation causes below and refer to the documentation.\n reads av. len clones clo/rds\n IGH -> 0 - 0 -\n IGH+ -> 0 - 0 -\n IGK -> 0 - 0 -\n IGK+ -> 0 - 0 -\n IGL -> 0 - 0 -\n TRA -> 0 - 0 -\n TRA+D -> 0 - 0 -\n TRB -> 0 - 0 -\n TRB+ -> 0 - 0 -\n TRD -> 0 - 0 -\n TRD+ -> 0 - 0 -\n TRG -> 0 - 0 -\n\n SEG -> 0 -\n SEG_+ -> 0 -\n SEG_- -> 0 -\n\n UNSEG too short -> 1 10.0\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": [
"small_V.fa"
],
"producer": [
"vidjil dev 4bf557b (2016-03-18)"
],
"run_timestamp": [
"2016-06-22 18:43:32"
]
},
"similarity": null,
"vidjil_json_version": "2014.10"
}
\ No newline at end of file
!LAUNCH: python ../fuse.py ../../data/no_clones.vidjil ../../data/results-two-clones-1-2.vidjil -o fused_no_clones.vidjil; cat fused_no_clones.vidjil
$ Fuse the three files
2: ListWindows: .0, 1000.
$ Check the producer string in output file
1: "producer": "vidjil fuse"
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