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Commit 0c680733 authored by Mikaël Salson's avatar Mikaël Salson Committed by Mathieu Giraud
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repseq_vdj.py: Why limiting to 100? 

When putting all files together, we have more than 100 sequences
parent 1c202809
Pipeline #63426 passed with stages
in 38 minutes and 26 seconds
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algo/tests/repseq_vdj.py
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...@@ -249,7 +249,7 @@ def header_igblast_results(ff_fasta, ff_igblast): ...@@ -249,7 +249,7 @@ def header_igblast_results(ff_fasta, ff_igblast):
### Vidjil ### Vidjil
VIDJIL_FINE = '{directory}/vidjil-algo -X 100 --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s' VIDJIL_FINE = '{directory}/vidjil-algo --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_KMER = '{directory}/vidjil-algo -w 20 --header-sep "#" -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_KMER = '{directory}/vidjil-algo -w 20 --header-sep "#" -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): def should_results_from_vidjil_output(f_log):
......
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