rbbt-util 5.44.1 → 6.0.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +2 -2
- data/etc/app.d/semaphores.rb +3 -3
- data/lib/rbbt/annotations/annotated_array.rb +207 -207
- data/lib/rbbt/annotations/refactor.rb +27 -0
- data/lib/rbbt/annotations/util.rb +282 -282
- data/lib/rbbt/annotations.rb +343 -320
- data/lib/rbbt/association/database.rb +200 -225
- data/lib/rbbt/association/index.rb +294 -291
- data/lib/rbbt/association/item.rb +227 -227
- data/lib/rbbt/association/open.rb +35 -34
- data/lib/rbbt/association/util.rb +0 -169
- data/lib/rbbt/association.rb +2 -4
- data/lib/rbbt/entity/identifiers.rb +119 -118
- data/lib/rbbt/entity/refactor.rb +12 -0
- data/lib/rbbt/entity.rb +319 -315
- data/lib/rbbt/hpc/batch.rb +72 -53
- data/lib/rbbt/hpc/lsf.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
- data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
- data/lib/rbbt/hpc/orchestrate.rb +19 -13
- data/lib/rbbt/hpc/slurm.rb +18 -18
- data/lib/rbbt/knowledge_base/entity.rb +13 -5
- data/lib/rbbt/knowledge_base/query.rb +2 -2
- data/lib/rbbt/knowledge_base/registry.rb +32 -31
- data/lib/rbbt/knowledge_base/traverse.rb +1 -1
- data/lib/rbbt/knowledge_base.rb +1 -1
- data/lib/rbbt/monitor.rb +36 -25
- data/lib/rbbt/persist/refactor.rb +166 -0
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
- data/lib/rbbt/persist/tsv.rb +187 -185
- data/lib/rbbt/persist.rb +556 -551
- data/lib/rbbt/refactor.rb +20 -0
- data/lib/rbbt/resource/path/refactor.rb +178 -0
- data/lib/rbbt/resource/path.rb +317 -497
- data/lib/rbbt/resource/util.rb +0 -48
- data/lib/rbbt/resource.rb +3 -390
- data/lib/rbbt/tsv/accessor.rb +2 -838
- data/lib/rbbt/tsv/attach.rb +303 -299
- data/lib/rbbt/tsv/change_id.rb +244 -245
- data/lib/rbbt/tsv/csv.rb +87 -85
- data/lib/rbbt/tsv/dumper.rb +2 -100
- data/lib/rbbt/tsv/excel.rb +26 -24
- data/lib/rbbt/tsv/field_index.rb +4 -1
- data/lib/rbbt/tsv/filter.rb +3 -2
- data/lib/rbbt/tsv/index.rb +2 -284
- data/lib/rbbt/tsv/manipulate.rb +750 -747
- data/lib/rbbt/tsv/marshal.rb +3 -3
- data/lib/rbbt/tsv/matrix.rb +2 -2
- data/lib/rbbt/tsv/parallel/through.rb +2 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
- data/lib/rbbt/tsv/parser.rb +678 -678
- data/lib/rbbt/tsv/refactor.rb +195 -0
- data/lib/rbbt/tsv/stream.rb +253 -251
- data/lib/rbbt/tsv/util.rb +420 -420
- data/lib/rbbt/tsv.rb +210 -208
- data/lib/rbbt/util/R/eval.rb +4 -4
- data/lib/rbbt/util/R/plot.rb +62 -166
- data/lib/rbbt/util/R.rb +21 -18
- data/lib/rbbt/util/cmd.rb +2 -318
- data/lib/rbbt/util/color.rb +269 -269
- data/lib/rbbt/util/colorize.rb +89 -89
- data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
- data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
- data/lib/rbbt/util/concurrency/processes.rb +389 -386
- data/lib/rbbt/util/config.rb +169 -167
- data/lib/rbbt/util/iruby.rb +20 -0
- data/lib/rbbt/util/log/progress/report.rb +241 -241
- data/lib/rbbt/util/log/progress/util.rb +99 -99
- data/lib/rbbt/util/log/progress.rb +102 -102
- data/lib/rbbt/util/log/refactor.rb +49 -0
- data/lib/rbbt/util/log.rb +486 -532
- data/lib/rbbt/util/migrate.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
- data/lib/rbbt/util/misc/development.rb +12 -11
- data/lib/rbbt/util/misc/exceptions.rb +117 -112
- data/lib/rbbt/util/misc/format.rb +2 -230
- data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
- data/lib/rbbt/util/misc/inspect.rb +2 -476
- data/lib/rbbt/util/misc/lock.rb +109 -106
- data/lib/rbbt/util/misc/omics.rb +9 -1
- data/lib/rbbt/util/misc/pipes.rb +765 -793
- data/lib/rbbt/util/misc/refactor.rb +20 -0
- data/lib/rbbt/util/misc/ssw.rb +27 -17
- data/lib/rbbt/util/misc/system.rb +0 -15
- data/lib/rbbt/util/misc.rb +39 -20
- data/lib/rbbt/util/named_array/refactor.rb +4 -0
- data/lib/rbbt/util/named_array.rb +3 -220
- data/lib/rbbt/util/open/refactor.rb +7 -0
- data/lib/rbbt/util/open.rb +3 -857
- data/lib/rbbt/util/procpath.rb +6 -6
- data/lib/rbbt/util/python/paths.rb +27 -0
- data/lib/rbbt/util/python/run.rb +115 -0
- data/lib/rbbt/util/python/script.rb +110 -0
- data/lib/rbbt/util/python/util.rb +3 -3
- data/lib/rbbt/util/python.rb +22 -81
- data/lib/rbbt/util/semaphore.rb +152 -148
- data/lib/rbbt/util/simpleopt.rb +9 -8
- data/lib/rbbt/util/ssh/refactor.rb +19 -0
- data/lib/rbbt/util/ssh.rb +122 -118
- data/lib/rbbt/util/tar.rb +117 -115
- data/lib/rbbt/util/tmpfile.rb +69 -67
- data/lib/rbbt/util/version.rb +2 -0
- data/lib/rbbt/workflow/refactor/entity.rb +11 -0
- data/lib/rbbt/workflow/refactor/export.rb +66 -0
- data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
- data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
- data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
- data/lib/rbbt/workflow/refactor.rb +153 -0
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
- data/lib/rbbt/workflow/remote_workflow.rb +6 -1
- data/lib/rbbt/workflow/step/run.rb +766 -766
- data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
- data/lib/rbbt/workflow/step.rb +2 -362
- data/lib/rbbt/workflow/task.rb +118 -118
- data/lib/rbbt/workflow/usage.rb +289 -287
- data/lib/rbbt/workflow/util/archive.rb +6 -5
- data/lib/rbbt/workflow/util/data.rb +1 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
- data/lib/rbbt/workflow/util/trace.rb +79 -44
- data/lib/rbbt/workflow.rb +4 -882
- data/lib/rbbt-util.rb +21 -13
- data/lib/rbbt.rb +16 -3
- data/python/rbbt/__init__.py +19 -1
- data/share/Rlib/plot.R +37 -37
- data/share/Rlib/svg.R +22 -5
- data/share/install/software/lib/install_helpers +1 -1
- data/share/rbbt_commands/hpc/list +2 -3
- data/share/rbbt_commands/hpc/orchestrate +4 -4
- data/share/rbbt_commands/hpc/tail +2 -0
- data/share/rbbt_commands/hpc/task +10 -7
- data/share/rbbt_commands/lsf/list +2 -3
- data/share/rbbt_commands/lsf/orchestrate +4 -4
- data/share/rbbt_commands/lsf/tail +2 -0
- data/share/rbbt_commands/lsf/task +10 -7
- data/share/rbbt_commands/migrate +1 -1
- data/share/rbbt_commands/pbs/list +2 -3
- data/share/rbbt_commands/pbs/orchestrate +4 -4
- data/share/rbbt_commands/pbs/tail +2 -0
- data/share/rbbt_commands/pbs/task +10 -7
- data/share/rbbt_commands/resource/produce +8 -1
- data/share/rbbt_commands/slurm/list +2 -3
- data/share/rbbt_commands/slurm/orchestrate +4 -4
- data/share/rbbt_commands/slurm/tail +2 -0
- data/share/rbbt_commands/slurm/task +10 -7
- data/share/rbbt_commands/system/clean +5 -5
- data/share/rbbt_commands/system/status +5 -5
- data/share/rbbt_commands/tsv/get +2 -3
- data/share/rbbt_commands/tsv/info +10 -13
- data/share/rbbt_commands/tsv/keys +18 -14
- data/share/rbbt_commands/tsv/slice +2 -2
- data/share/rbbt_commands/tsv/transpose +6 -2
- data/share/rbbt_commands/workflow/info +20 -24
- data/share/rbbt_commands/workflow/list +1 -1
- data/share/rbbt_commands/workflow/prov +20 -13
- data/share/rbbt_commands/workflow/server +11 -1
- data/share/rbbt_commands/workflow/task +76 -71
- data/share/rbbt_commands/workflow/write_info +26 -9
- data/share/software/opt/ssw/ssw.c +861 -0
- data/share/software/opt/ssw/ssw.h +130 -0
- data/share/workflow_config.ru +3 -3
- metadata +40 -2
data/lib/rbbt/util/misc/omics.rb
CHANGED
|
@@ -258,7 +258,7 @@ module Misc
|
|
|
258
258
|
alt = m[3]
|
|
259
259
|
alt = "*" if alt == "Ter"
|
|
260
260
|
ref = THREE_TO_ONE_AA_CODE[ref.downcase]
|
|
261
|
-
alt =
|
|
261
|
+
alt = (alt == "Ter" || alt == "*") ? "*" : THREE_TO_ONE_AA_CODE[alt.downcase]
|
|
262
262
|
mutation = [ref, num, alt] * ""
|
|
263
263
|
end
|
|
264
264
|
one_aa_code = THREE_TO_ONE_AA_CODE.values
|
|
@@ -575,4 +575,12 @@ module Misc
|
|
|
575
575
|
[chr, pos.to_i - 1, pos.to_i - 1 + size, mutation] * "\t"
|
|
576
576
|
end
|
|
577
577
|
end
|
|
578
|
+
|
|
579
|
+
def self.sort_mutation_stream_strict(stream, sep=":")
|
|
580
|
+
CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -V -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
|
|
581
|
+
end
|
|
582
|
+
|
|
583
|
+
def self.sort_mutation_stream(stream, sep=":")
|
|
584
|
+
CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
|
|
585
|
+
end
|
|
578
586
|
end
|