Commit 9ef93faa authored by Mikaël Salson's avatar Mikaël Salson
Browse files

germline: Changes in IMGT germlines.

4 genes added in IGHV (welcome on board): IGHV3-30-22, IGHV3-30-33, IGHV3-30-42, IGHV3-30-52.
5 IGKV genes removed (IGKV3-NL[1-5]) and 2 added (IGKV3D-11, IGKV3D-20)
parent b063950e
...@@ -4,9 +4,9 @@ ...@@ -4,9 +4,9 @@
$ Check md5 in germline/, sequences split from IMGT $ Check md5 in germline/, sequences split from IMGT
1:3a655c9d99ca04907a120f1b69febf2e IGHD.fa 1:3a655c9d99ca04907a120f1b69febf2e IGHD.fa
1:0d87f672c582e7e15cdcaa0fb5e08f6f IGHJ.fa 1:0d87f672c582e7e15cdcaa0fb5e08f6f IGHJ.fa
1:7451e8a88f0add1dc7e028ac907327fc IGHV.fa 1:4f43acd99f6285d3039e2626ed753c8a IGHV.fa
1:6a696e7cc21b8ffb7e3adbcf37167711 IGKJ.fa 1:6a696e7cc21b8ffb7e3adbcf37167711 IGKJ.fa
1:825e0f293ae564be41f7142a85d21b44 IGKV.fa 1:2746f12c8af2a9b42b166ef468dd08d9 IGKV.fa
1:a6bdc2aa82d151e30d10d302559355b6 IGLJ.fa 1:a6bdc2aa82d151e30d10d302559355b6 IGLJ.fa
1:6012b3ce22ce0a669ba1b8e670bd2db1 IGLV.fa 1:6012b3ce22ce0a669ba1b8e670bd2db1 IGLV.fa
1:17513843a8d4d2025c38afa13249e2e1 TRAJ.fa 1:17513843a8d4d2025c38afa13249e2e1 TRAJ.fa
......
...@@ -4,14 +4,14 @@ $ number of reads and kmers ...@@ -4,14 +4,14 @@ $ number of reads and kmers
1:13153 reads, 3020179 kmers 1:13153 reads, 3020179 kmers
$ k-mers, IGHV $ k-mers, IGHV
1:13115 .* 1223118 .*IGHV 1:13115 .* 1222841 .*IGHV
$ k-mers, IGHJ $ k-mers, IGHJ
1:38 .* 435867 .*IGHJ 1:38 .* 435867 .*IGHJ
$ k-mers, ambiguous $ k-mers, ambiguous
1:47370 .*\\? 1:47648 .*\\?
$ k-mers, unknown $ k-mers, unknown
1:1251710 .*_ 1:1251709 .*_
...@@ -2,10 +2,10 @@ ...@@ -2,10 +2,10 @@
!LOG: stanford-w100.log !LOG: stanford-w100.log
$ Find the good number of "too short sequences" for windows of size 100 $ Find the good number of "too short sequences" for windows of size 100
1: UNSEG too short w -> 2217 1: UNSEG too short w -> 2221
$ Find the good number of segmented sequences (including "too short sequences") $ Find the good number of segmented sequences (including "too short sequences")
1: junction detected in 13148 reads .100%. 1: junction detected in 13148 reads .100%.
$ Find the good number of windows of size 100 in Stanford S22 $ Find the good number of windows of size 100 in Stanford S22
1: found 9800 100-windows in 10931 reads 1: found 9796 100-windows in 10927 reads
!LAUNCH: ../../vidjil -V ../../germline/IGHV.fa -D ../../germline/IGHD.fa -J ../../germline/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# ../../data/Stanford_S22.fasta !LAUNCH: ../../vidjil -V ../../germline/IGHV.fa -D ../../germline/IGHD.fa -J ../../germline/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# ../../data/Stanford_S22.fasta
$ Parses IGHV.fa germline $ Parses IGHV.fa germline
1: 100439 bp in 344 sequences 1: 101627 bp in 348 sequences
$ Parses IGHD.fa germline $ Parses IGHD.fa germline
1: 1070 bp in 44 sequences 1: 1070 bp in 44 sequences
......
...@@ -28,7 +28,7 @@ void testOnlineFasta1() { ...@@ -28,7 +28,7 @@ void testOnlineFasta1() {
void testFastaNbSequences() { void testFastaNbSequences() {
TAP_TEST(nb_sequences_in_fasta("../../germline/IGHV.fa") == 344, TEST_FASTA_NB_SEQUENCES, "ccc"); TAP_TEST(nb_sequences_in_fasta("../../germline/IGHV.fa") == 348, TEST_FASTA_NB_SEQUENCES, "ccc");
int a1 = approx_nb_sequences_in_fasta("../../germline/IGHV.fa"); int a1 = approx_nb_sequences_in_fasta("../../germline/IGHV.fa");
TAP_TEST(a1 >= 340 && a1 <= 348, TEST_FASTA_NB_SEQUENCES, ""); TAP_TEST(a1 >= 340 && a1 <= 348, TEST_FASTA_NB_SEQUENCES, "");
......
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