Commit 3c181cf9 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Mathieu Giraud

tests: testing multi-germline segmentation

multi-complete.fa -> 7 reads (1 per system), exact concatenation V+(D)+J, no deletion, no insertion
multi-short.fa -> the same 7 reads, but shortened (especially at V end)
parent c42602db
!LAUNCH: ../../vidjil -g ../../germline ../../data/multi-complete.fa
$ Segment all the seven reads
1:segmented 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
$ Segment one read on TRB
1:TRB .* -> .* 1
$ Segment one read on TRG
1:TRG .* -> .* 1
$ Segment one read on TRD
1:TRD .* -> .* 1
$ Segment one read on IGH
1:IGH .* -> .* 1
$ Segment one read on IGK
1:IGK .* -> .* 1
$ Segment one read on IGL
1:IGL .* -> .* 1
!LAUNCH: ../../vidjil -g ../../germline ../../data/multi-short.fa
$ Segment all the seven reads
1:segmented 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
$ Segment one read on TRB
1:TRB .* -> .* 1
$ Segment one read on TRG
1:TRG .* -> .* 1
$ Segment one read on TRD
1:TRD .* -> .* 1
$ Segment one read on IGH
1:IGH .* -> .* 1
$ Segment one read on IGK
1:IGK .* -> .* 1
$ Segment one read on IGL
1:IGL .* -> .* 1
>TRA--V1-1*01--J1*01
ggacaaagccttgagcagccctctgaagtgacagctgtggaaggagccattgtccagata
aactgcacgtaccagacatctgggttttatgggctgtcctggtaccagcaacatgatggc
ggagcacccacatttctttcttacaatgctctggatggtttggaggagacaggtcgtttt
tcttcattccttagtcgctctgatagttatggttacctccttctacaggagctccagatg
aaagactctgcctcttacttctgcgctgtgagaga
gtatgaaagtattacctcccagttgcaatttggcaaaggaaccagagtttccacttctcc
cc
>TRB--V1*01--D1*01--J1-1*01
gatactggaattacccagacaccaaaatacctggtcacagcaatggggagtaaaaggaca
atgaaacgtgagcatctgggacatgattctatgtattggtacagacagaaagctaagaaa
tccctggagttcatgttttactacaactgtaaggaattcattgaaaacaagactgtgcca
aatcacttcacacctgaatgccctgacagctctcgcttataccttcatgtggtcgcactg
cagcaagaagactcagctgcgtatctctgcaccagcagccaaga
gggacagggggc
tgaacactgaagctttctttggacaaggcaccagactcacagttgtag
>TRG--V1*01--J1*01
tcttccaacttggaagggagaacgaagtcagtcaccaggctgactgggtcatctgctgaa
atcacctgtgatcttcctggagcaagtaccttatacatccactggtacctgcaccaggag
gggaaggccccacagtgtcttctgtactatgaaccctactactccagggttgtgctggaa
tcaggaatcactccaggaaagtatgacactggaagcacaaggagcaattggaatttgaga
ctgcaaaatctaattaaaaatgattctgggttctattactgtgccacctgggacagg
gaattattataagaaactctttggcagtggaacaacactggttgtcacag
>TRD--V1*01--D1*01--J1*01
gcccagaaggttactcaagcccagtcatcagtatccatgccagtgaggaaagcagtcacc
ctgaactgcctgtatgaaacaagttggtggtcatattatattttttggtacaagcaactt
cccagcaaagagatgattttccttattcgccagggttctgatgaacagaatgcaaaaagt
ggtcgctattctgtcaacttcaagaaagcagcgaaatccgtcgccttaaccatttcagcc
ttacagctagaagattcagcaaagtacttttgtgctcttggggaact
gaaatagt
acaccgataaactcatctttggaaaaggaacccgtgtgactgtggaaccaa
>IGH--V1-18*01--D1-1*01--J1*01
caggttcagctggtgcagtctggagctgaggtgaagaagcctggggcctcagtgaaggtc
tcctgcaaggcttctggttacacctttaccagctatggtatcagctgggtgcgacaggcc
cctggacaagggcttgagtggatgggatggatcagcgcttacaatggtaacacaaactat
gcacagaagctccagggcagagtcaccatgaccacagacacatccacgagcacagcctac
atggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
ggtacaactggaacgac
gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag
>IGK--V1-12*01--J1*01
gacatccagatgacccagtctccatcttccgtgtctgcatctgtaggagacagagtcacc
atcacttgtcgggcgagtcagggtattagcagctggttagcctggtatcagcagaaacca
gggaaagcccctaagctcctgatctatgctgcatccagtttgcaaagtggggtcccatca
aggttcagcggcagtggatctgggacagatttcactctcaccatcagcagcctgcagcct
gaagattttgcaacttactattgtcaacaggctaacagtttccctcc
gtggacgttcggccaagggaccaaggtggaaatcaaac
>IGL--V1-36*01--J1*01
cagtctgtgctgactcagccaccctcggtgtctgaagcccccaggcagagggtcaccatc
tcctgttctggaagcagctccaacatcggaaataatgctgtaaactggtaccagcagctc
ccaggaaaggctcccaaactcctcatctattatgatgatctgctgccctcaggggtctct
gaccgattctctggctccaagtctggcacctcagcctccctggccatcagtgggctccag
tctgaggatgaggctgattattactgtgcagcatgggatgacagcctgaatggtcc
ttatgtcttcggaactgggaccaaggtcaccgtcctag
>TRA--V1-1*01--J1*01
tcttcattccttagtcgctctgatagttatggttacctccttctacaggagctccagatg
aaagactctgcctcttacttctgcgctgtgagaga
gtatgaaagtattacctcccagttgcaatttggcaaaggaaccagagtttccacttctcc
>TRB--V1*01--D1*01--J1-1*01
cagcaagaagactcagctgcgtatctctgcaccagcagccaaga
gggacagggggc
tgaacactgaagctttctttggacaaggcaccagactcacagttgtag
>TRG--V1*01--J1*01
ctgcaaaatctaattaaaaatgattctgggttctattactgtgccacctgggacagg
gaattattataagaaactctttggcagtggaacaacactggttgtcacag
>TRD--V1*01--D1*01--J1*01
ttacagctagaagattcagcaaagtacttttgtgctcttggggaact
gaaatagt
acaccgataaactcatctttggaaaaggaacccgtgtgactgtggaaccaa
>IGH--V1-18*01--D1-1*01--J1*01
atggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
ggtacaactggaacgac
gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag
>IGK--V1-12*01--J1*01
gaagattttgcaacttactattgtcaacaggctaacagtttccctcc
gtggacgttcggccaagggaccaaggtggaaatcaaac
>IGL--V1-36*01--J1*01
tctgaggatgaggctgattattactgtgcagcatgggatgacagcctgaatggtcc
ttatgtcttcggaactgggaccaaggtcaccgtcctag
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