From db1d9c8ddfb06e6b56c82dbc96a2266acc372902 Mon Sep 17 00:00:00 2001 From: gnefedev <14794051+gnefedev@users.noreply.github.com> Date: Thu, 31 Oct 2024 19:25:02 +0000 Subject: [PATCH] regression tests automated change --- regression/cli-help/exportReportsTable.txt | 4 +- .../cli-help/exportShmSingleCellTrees.txt | 64 ++++++++++++------- regression/cli-help/exportShmTrees.txt | 4 +- .../cli-help/exportShmTreesWithNodes.txt | 64 ++++++++++++------- 4 files changed, 88 insertions(+), 48 deletions(-) diff --git a/regression/cli-help/exportReportsTable.txt b/regression/cli-help/exportReportsTable.txt index d4afb0237..564351fd9 100644 --- a/regression/cli-help/exportReportsTable.txt +++ b/regression/cli-help/exportReportsTable.txt @@ -32,8 +32,8 @@ Export reports from files in tabular format. [report.tsv] Path where to write reports. Print in stdout if omitted. --without-upstreams Don't export upstream reports for sources of steps with several inputs, like `findShmTrees`. - -p, --preset Specify preset of export fields. Possible values: min, full. - -pf, --preset-file + --preset Specify preset of export fields. Possible values: min, full. + --preset-file Specify preset file of export fields --no-header Don't print first header line, print only data -f, --force-overwrite Force overwrite of output file(s). diff --git a/regression/cli-help/exportShmSingleCellTrees.txt b/regression/cli-help/exportShmSingleCellTrees.txt index f36859b8b..390b4466a 100644 --- a/regression/cli-help/exportShmSingleCellTrees.txt +++ b/regression/cli-help/exportShmSingleCellTrees.txt @@ -10,21 +10,24 @@ Usage: mixcr exportShmSingleCellTrees [--include-one-chain-trees] [--only-observ [-rootsCountPerChain] [-treeHeight] [-nodeId] [-isObserved] [-parentId] [-distance (germline|mrca|parent)]... [-vHit] [-jHit] [-vGene] [-jGene] [-vFamily] [-jFamily] [-nFeature - [(germline|mrca|parent)]]... [-allNFeatures - [(germline|mrca|parent)]]... [-aaFeature - [(germline|mrca|parent)]]... [-allAAFeatures - [(germline|mrca|parent)]]... [-nFeatureImputed - [(germline|mrca|parent)]]... [-allNFeaturesImputed - [ ] - [(germline|mrca|parent)]]... [-aaFeatureImputed - [(germline|mrca|parent)]]... - [-allAAFeaturesImputed [ - ] [(germline|mrca|parent)]]... [-nLength - [(germline|mrca|parent)]]... - [-allNLength [(germline|mrca|parent)]]... [-aaLength - [(germline|mrca|parent)]]... - [-allAALength [(germline|mrca|parent)]]... [-nMutations [(germline|mrca|parent)] + [withAlignmentGaps]]... [-allNFeatures + [(germline|mrca|parent)] [withAlignmentGaps]]... [-aaFeature + [(germline|mrca|parent)] + [withAlignmentGaps]]... [-allAAFeatures + [(germline|mrca|parent)] [withAlignmentGaps]]... + [-nFeatureImputed [(germline|mrca|parent)]]... + [-allNFeaturesImputed [ + ] [(germline|mrca|parent)]]... + [-aaFeatureImputed + [(germline|mrca|parent)]]... [-allAAFeaturesImputed + [ ] + [(germline|mrca|parent)]]... [-nLength [(germline|mrca|parent)]]... [-allNLength + [(germline|mrca|parent)]]... [-aaLength [(germline|mrca|parent)]]... [-allAALength + [(germline|mrca|parent)]]... [-nMutations + [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]]... [-allNMutations [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]]... @@ -57,8 +60,10 @@ Usage: mixcr exportShmSingleCellTrees [--include-one-chain-trees] [--only-observ gene_feature]...>] [(substitutions|indels|inserts|deletions)]]... [-aaMutationsRate [] - [(substitutions|indels|inserts|deletions)]]... [-isotype - [(primary|subclass|auto)]]... [-cellId + [(substitutions|indels|inserts|deletions)]]... [-pN + []]... [-pS []]... [-pNpS []]... [-isotype [(primary|subclass|auto)]]... [-cellId [(none|space|dash)]]... [-uniqueTagCount (Molecule|Cell|Sample)]... [-cellGroup] [-hasStops ]... [-isOOF ]... [-isProductive @@ -84,8 +89,8 @@ separate columns. Initial data for building tree should contain cell data. --ids [,...] Filter specific trees by id --chains Export only trees that contains clones with specific chain (e.g. IGK, IGL or IGH). - -p, --preset Specify preset of export fields. Possible values: min, default. - -pf, --preset-file + --preset Specify preset of export fields. Possible values: min, default. + --preset-file Specify preset file of export fields --cell-type ... Export SHM trees for given cell type. By default all will be exported. @@ -140,19 +145,19 @@ Possible fields to export -jGene Export best J hit gene name (e.g. TRBV12-3 for TRBV12-3*00) -vFamily Export best V hit family name (e.g. TRBV12 for TRBV12-3*00) -jFamily Export best J hit family name (e.g. TRBV12 for TRBV12-3*00) - -nFeature [(germline|mrca|parent)] + -nFeature [(germline|mrca|parent)] [withAlignmentGaps] Export nucleotide sequence of specified gene feature. If second arg is omitted, then feature will be printed for current node. Otherwise - for corresponding `parent`, `germline` or `mrca`. - -allNFeatures [(germline|mrca|parent)] + -allNFeatures [(germline|mrca|parent)] [withAlignmentGaps] Export nucleotide sequences for all covered gene features. If first arg is omitted, then feature will be printed for current node. Otherwise - for corresponding `parent`, `germline` or `mrca`. - -aaFeature [(germline|mrca|parent)] + -aaFeature [(germline|mrca|parent)] [withAlignmentGaps] Export amino acid sequence of specified gene feature. If second arg is omitted, then feature will be printed for current node. Otherwise - for corresponding `parent`, `germline` or `mrca`. - -allAAFeatures [(germline|mrca|parent)] + -allAAFeatures [(germline|mrca|parent)] [withAlignmentGaps] Export amino acid sequences for all covered gene features. If first arg is omitted, then feature will be printed for current node. Otherwise - for corresponding `parent`, `germline` or `mrca`. @@ -308,6 +313,21 @@ Possible fields to export Resolutions of wildcards in CDR3 are excluded from calculation. Second parameter will filter mutations by type, by default no filtering. + -pN [] + Count of non-synonymous substitutions normalized by total count of + possible non-synonymous substitutions. By default, will be used all + covered features. For wildcards in VJJunction all possible + combinations will be calculated and averaged. + -pS [] + Count of synonymous substitutions normalized by total count of + possible synonymous substitutions. By default, will be used all + covered features. For wildcards in VJJunction all possible + combinations will be calculated and averaged. + -pNpS [] + Ration of pN to pS. In case of no mutations value will be absent.By + default, will be used all covered features. For wildcards in + VJJunction all possible combinations will be calculated and + averaged. If pN or pS is zero, no value will be exported. -isotype [(primary|subclass|auto)] Export isotype for IGH chains if it's can be distinguishable. `primary` will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. `subtype` diff --git a/regression/cli-help/exportShmTrees.txt b/regression/cli-help/exportShmTrees.txt index e6a886ae2..db30bf4bc 100644 --- a/regression/cli-help/exportShmTrees.txt +++ b/regression/cli-help/exportShmTrees.txt @@ -26,9 +26,9 @@ data) --ids [,...] Filter specific trees by id --chains Export only trees that contains clones with specific chain (e.g. IGK, IGL or IGH). - -p, --preset Specify preset of export fields. Possible values: default, + --preset Specify preset of export fields. Possible values: default, defaultSingleCell, min. - -pf, --preset-file + --preset-file Specify preset file of export fields --no-header Don't print first header line, print only data --not-covered-as-empty Export not covered regions as empty text. diff --git a/regression/cli-help/exportShmTreesWithNodes.txt b/regression/cli-help/exportShmTreesWithNodes.txt index 3bbbdf0ab..868bd2036 100644 --- a/regression/cli-help/exportShmTreesWithNodes.txt +++ b/regression/cli-help/exportShmTreesWithNodes.txt @@ -17,12 +17,14 @@ Usage: mixcr exportShmTreesWithNodes [--split-by-tags (Molecule|Cell|Sample)] [- [-dFamilies] [-jFamilies] [-cFamilies] [-vAlignment] [-dAlignment] [-jAlignment] [-cAlignment] [-vAlignments] [-dAlignments] [-jAlignments] [-cAlignments] [-nFeature - [(germline|mrca|parent)]]... [-allNFeatures - [(germline|mrca|parent)]]... [-qFeature ]... - [-allQFeatures [ + [(germline|mrca|parent)] + [withAlignmentGaps]]... [-allNFeatures + [(germline|mrca|parent)] [withAlignmentGaps]]... [-qFeature + ]... [-allQFeatures [ ]]... [-aaFeature - [(germline|mrca|parent)]]... [-allAAFeatures - [(germline|mrca|parent)]]... [-nFeatureImputed + [(germline|mrca|parent)] [withAlignmentGaps]]... + [-allAAFeatures [(germline|mrca|parent)] + [withAlignmentGaps]]... [-nFeatureImputed [(germline|mrca|parent)]]... [-allNFeaturesImputed [ ] [(germline|mrca|parent)]]... [-aaFeatureImputed @@ -82,17 +84,20 @@ Usage: mixcr exportShmTreesWithNodes [--split-by-tags (Molecule|Cell|Sample)] [- [-nMutationsRate [] [(substitutions|indels|inserts|deletions)]]... [-aaMutationsRate [] - [(substitutions|indels|inserts|deletions)]]... [-geneLabel -