Commit ff54d77b authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: add and update tests

Add a new test testing more systematically minimization clustering on trimmed reads.
Simplify the original test.
parent a6a48606
Pipeline #14463 passed with stages
in 20 minutes and 9 seconds
>cd19-1-100
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
# Shortened reads
>cd19-1-95
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGG
>cd19-1-90
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGA
>cd19-1-85
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTA
>cd19-1-80
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGT
>cd19-1-75
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGA
>cd19-1-70
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCC
>cd19-1-65
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCC
>cd19-1-60
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGA
>cd19-1-55
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAG
>cd19-1-50
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGC
>cd19-6-100
CCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-11-100
GTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-16-100
CCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-21-100
AGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-26-100
CCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-31-100
GTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-36-100
TGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-41-100
AGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-46-100
AGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-51-100
TGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGGGTCTG
>cd19-6-95
CCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGAGACGG
>cd19-11-90
GTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTAATGGA
>cd19-16-85
CCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGTGGGTA
>cd19-21-80
AGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGATATGT
>cd19-26-75
CCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCCAGAGA
......@@ -7,14 +7,6 @@ CCCCTCAGTGCAATGTAGGAGTCCAAGGGGTAAAAACATACAGGGGGGGAAGACCCTCTCCGT
GTCTCAGCTGGAGCTCCAGGATAGTGGCACCTGGACATGCACTGTCTTGCAGAACCAGAAGAAGGTGGAG
>read-CD4-exact-trimmed-60
GAGCTCCAGGATAGTGGCACCTGGACATGCACTGTCTTGCAGAACCAGAAGAAGGTGGAG
>read-CD4-exact-trimmed-55
CCAGGATAGTGGCACCTGGACATGCACTGTCTTGCAGAACCAGAAGAAGGTGGAG
>read-CD4-exact-trimmed-50
ATAGTGGCACCTGGACATGCACTGTCTTGCAGAACCAGAAGAAGGTGGAG
>read-CD19-exact-1
CTGGACCCATGTGCACCCCAAGGGGCCTAAGTCATTGCTGAGCCTAGAGCTGAAGGACGATCGCCCGGCC
AGAGATATGTGGGTAATGGAGACGGGTCTGTTGTTGCCCCGGGCCACAGCTCAAGACGCTGGAAAGTATT
......
!LAUNCH: $VIDJIL_DIR/$EXEC -a -g $VIDJIL_DIR/germline/homo-sapiens-cd.g -A $VIDJIL_DATA/cd-19-trimmed.fa
$ Load CD-sorting.fa
1:homo-sapiens/CD-sorting.fa .* 28 sequences
$ KmerSegmenter, do not map reads < 52bp
1: UNSEG too short w .* 3 .* 50.0
$ KmerSegmenter, map reads and gather some reads, including a large clone
1: found 9 50-windows in 23 reads
1:Clone .* 13 reads
$ FineSegmenter, find 9 clones with CD19
9:clone-.* CD19 .* SEG
......@@ -3,22 +3,18 @@
$ Load CD-sorting.fa
1:homo-sapiens/CD-sorting.fa .* 28 sequences
$ KmerSegmenter, do not map a read < 52bp
1: UNSEG too short w .* 1 .* 50.0
1: read-CD4-exact-trimmed-50 .* UNSEG too short w
$ KmerSegmenter, map reads
1: found 8 50-windows in 10 reads
1: found 6 50-windows in 8 reads
$ KmerSegmenter, cluster lightly trimmed reads with original ones
$ KmerSegmenter, cluster lightly trimmed or mutated reads with original ones
2:Clone .* 2 reads
$ KmerSegmenter, the above clusterisation come from coherent minimizing positions
$ KmerSegmenter, the above clusterisation comes from coherent minimizing positions
1:read-CD4-exact-1 .* @85
1:read-CD4-exact-trimmed .* @78
$ FineSegmenter, find 5 clones with CD4 and 3 with CD19
5:clone-00.* CD4 .* SEG
$ FineSegmenter, find 3 clones with CD4 and 3 with CD19
3:clone-00.* CD4 .* SEG
3:clone-00.* CD19 .* SEG
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