From d8d8a5e40d1cf1ae9bf363dde5c934d2473e368a Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Thu, 20 Apr 2023 12:21:36 +0200 Subject: [PATCH] udpate test dfam db --- .../test-data/Dfam_partial_test.h5 | Bin 4270800 -> 4310416 bytes tools/repeatmasker/test-data/README.md | 5 ++++- .../test-data/small_dfam_up.fasta.cat | 6 +++--- .../test-data/small_dfam_up.fasta.log | 2 +- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/tools/repeatmasker/test-data/Dfam_partial_test.h5 b/tools/repeatmasker/test-data/Dfam_partial_test.h5 index 9d45f717d60b38faf3ffa72075529c4d65ea98f8..3ff14db9602d41baab673b20c9acb47b0e5681ce 100644 GIT binary patch delta 38414 zcmcJ24M1GQwea2D#4Jk^7h?pH5H7?32>}+CpCypoOF|54V#tq*zpx=o76o?YCxFp{ z&$d#n6};9QXJB40CXul$Bs63_}c?|(Kbi6_U8KJP0Oed;3J@9 z0dykJ+0`2Apk(cFN5T5#@N*Gl$Nb#^$j{OnYP~BrT|__v*~J3cu|QXIXKT0{5h8HG zKE%tZUJ+Afl_=933io%m9uIa)`rT)%E?-Ew%XDj~y)x_sb_dg{6gF$U; zp33bd#f25+6&`On13-!}h<7bigmF&SfFuwW7kV&VLhfL2v6p04z!H!X7>GOYMuc*K 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https://github.com/Dfam-consortium/FamDB/ (commit: 20c436d) + +`./export_dfam.py --from-tax-dump /path/to/taxonomy_dump/from_ncbi/ --from-hmm test_data/Dfam_partial.hmm --db-version 1.0 Dfam_partial_test.h5` + diff --git a/tools/repeatmasker/test-data/small_dfam_up.fasta.cat b/tools/repeatmasker/test-data/small_dfam_up.fasta.cat index 5348981f5e6..6c09a24b667 100644 --- a/tools/repeatmasker/test-data/small_dfam_up.fasta.cat +++ b/tools/repeatmasker/test-data/small_dfam_up.fasta.cat @@ -98,6 +98,6 @@ Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.2-p1 , default mode -run with rmblastn version 2.10.0+ -RM Library: CONS-_ +RepeatMasker version 4.1.5 , default mode +run with rmblastn version 2.13.0+ +RM Library: CONS-Dfam_1.0 diff --git a/tools/repeatmasker/test-data/small_dfam_up.fasta.log b/tools/repeatmasker/test-data/small_dfam_up.fasta.log index 5411d17ef6c..0b437f356df 100644 --- a/tools/repeatmasker/test-data/small_dfam_up.fasta.log +++ b/tools/repeatmasker/test-data/small_dfam_up.fasta.log @@ -1,4 +1,4 @@ -SW scoret% div.t% del.t% ins.tquery sequencetpos in query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID +SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID 18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2