Commit 440df9cd authored by Mathieu Giraud's avatar Mathieu Giraud

tests, should-vdj-to-tap.py, repseq_vdj.py: vidjil-algo

parent 5972737b
Pipeline #14003 passed with stages
in 17 seconds
......@@ -249,12 +249,12 @@ def header_igblast_results(ff_fasta, ff_igblast):
### Vidjil
VIDJIL_FINE = '{directory}/vidjil -X 100 -# "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_KMER = '{directory}/vidjil -w 20 -# "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
VIDJIL_FINE = '{directory}/vidjil-algo -X 100 -# "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_KMER = '{directory}/vidjil-algo -w 20 -# "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
def should_results_from_vidjil_output(f_log):
'''
Yield (should, result) couples from a Vidjil output including lines in the form of:
Yield (should, result) couples from a Vidjil-algo output including lines in the form of:
>TRDD2*01_1/AGG/1_TRDD3*01__TRD+ + VJ 0 84 88 187 TRDD2*01 1/AGG/1 TRDD3*01 TRD+
or
>TRDV3*01_0//0_TRDJ4*01 ! + VJ 0 49 50 97 TRD UNSEG noisy
......
......@@ -6,7 +6,7 @@ A .should-vdj.fa file is a fasta file whose identifiers are in the form:
The 'should_pattern' describes the expected V(D)J segmentation in a .vdj format.
All spaces is the pattern have to be replaced by '_'.
The script launches Vidjil (or any other PROGRAM) on the .shoud-vdj.fasta file,
The script launches vidjil-algo (or any other PROGRAM) on the .shoud-vdj.fasta file,
expecting that it returns another fasta file whose identifiers are in the form:
>should_pattern result
......
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