Commit 379aecd1 authored by Mikael Salson's avatar Mikael Salson Committed by Mathieu Giraud

should-get-tests: Ambiguous representative computation

We should find representatives even despite sequencing errors.

Currently this is not the case for the first clone, probably
because the seeds are not sensitive enough.
parent ff80c5a8
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/test_representatives.fa
$ Three clones should be found
1:3 clones
# All clones should have a representative on 100% of the length
# Each regex should appear twice as it also appears in the similarity matrix.
$ Representative length of clone 1
f2:clone1.*100% of
$ Representative length of clone 2
2:clone2.*100% of
$ Representative length of clone 3
2:clone3.*100% of
>clone1-1
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacggGcCtgtattactgtgccaggggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone1-2
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaCcggccTtgtattactgtgccaggggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone1-3
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacggAcAtgtattactgtgccaggggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone1-4
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaGcggccgtgtattactgtgccaggggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone1-5
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacggTcgtgtattactgtgccaggggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone2-1
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacgggccAgtattactgtgccaggggggggggtacatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone2-2
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacgggccAgtattactgtgccaggggggggggtacatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone2-3
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacgggTctgtattactgtgccaggggggggggtacatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone2-4
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacggCcctgtattactgtgccaggggggggggtacatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone2-5
gtgctgacctgcggggtggcacagcccctaaaaaaagcttcgagttatggccgggtctctcccctctctctgtcaaactcaacctgctcaggaagttccagggctgtgtctcgattacgcctgacgaatccacgggcgctggctacagggagctgagtagcctgagttgtgaggaaacggCcctgtattactgtgccaggggggggggtacatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone3-1
ccagtcccaggtgcagctggtgcagtctggggctgaggtgaagaagcctgggtcctcggtgaaggtctcctgcaaggcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcaCctgCgaActgaggacacggccgtgtattactgtgccagggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone3-2
ccagtcccaggtgcagctggtgcagtctggggctgaggtgaagaagcctgggtcctcggtgaaggtctcctgcaaggcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcCgagaActgaggacacggccgtgtattactgtgccagggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone3-3
ccagtcccaggtgcagctggtgcagtctggggctgaggtgaagaagcctgggtcctcggtgaaggtctcctgcaaggcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcaCctgCgatctgaggacacggccgtgtattactgtgccagggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone3-4
ccagtcccaggtgcagctggtgcagtctggggctgaggtgaagaagcctgggtcctcggtgaaggtctcctgcaaggcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcaCctgTgatctgaggacacggccgtgtattactgtgccagggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
>clone3-5
ccagtcccaggtgcagctggtgcagtctggggctgaggtgaagaagcctgggtcctcggtgaaggtctcctgcaaggcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcaTctgCgatctgaggacacggccgtgtattactgtgccagggggggggtacgatttttggagtggttattatccaaactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcaggtaag
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