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Merge pull request #1845 from milaboratory/mixcr-regression-tests/exp…
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…orts-for-trees

Regression tests changes in the exports-for-trees
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@gnefedev
gnefedev authored Oct 31, 2024
2 parents 82cdf2f + db1d9c8 commit ea49a4f
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4 changes: 2 additions & 2 deletions regression/cli-help/exportReportsTable.txt
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Expand Up @@ -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 <preset> Specify preset of export fields. Possible values: min, full.
-pf, --preset-file <presetFile>
--preset <preset> Specify preset of export fields. Possible values: min, full.
--preset-file <presetFile>
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).
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64 changes: 42 additions & 22 deletions regression/cli-help/exportShmSingleCellTrees.txt
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Expand Up @@ -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
<gene_feature> [(germline|mrca|parent)]]... [-allNFeatures
[(germline|mrca|parent)]]... [-aaFeature <gene_feature>
[(germline|mrca|parent)]]... [-allAAFeatures
[(germline|mrca|parent)]]... [-nFeatureImputed <gene_feature>
[(germline|mrca|parent)]]... [-allNFeaturesImputed
[<from_reference_point> <to_reference_point>]
[(germline|mrca|parent)]]... [-aaFeatureImputed
<gene_feature> [(germline|mrca|parent)]]...
[-allAAFeaturesImputed [<from_reference_point>
<to_reference_point>] [(germline|mrca|parent)]]... [-nLength
<gene_feature[,gene_feature]...> [(germline|mrca|parent)]]...
[-allNLength [(germline|mrca|parent)]]... [-aaLength
<gene_feature[,gene_feature]...> [(germline|mrca|parent)]]...
[-allAALength [(germline|mrca|parent)]]... [-nMutations
<gene_feature> [(germline|mrca|parent)]
[withAlignmentGaps]]... [-allNFeatures
[(germline|mrca|parent)] [withAlignmentGaps]]... [-aaFeature
<gene_feature> [(germline|mrca|parent)]
[withAlignmentGaps]]... [-allAAFeatures
[(germline|mrca|parent)] [withAlignmentGaps]]...
[-nFeatureImputed <gene_feature> [(germline|mrca|parent)]]...
[-allNFeaturesImputed [<from_reference_point>
<to_reference_point>] [(germline|mrca|parent)]]...
[-aaFeatureImputed <gene_feature>
[(germline|mrca|parent)]]... [-allAAFeaturesImputed
[<from_reference_point> <to_reference_point>]
[(germline|mrca|parent)]]... [-nLength <gene_feature[,
gene_feature]...> [(germline|mrca|parent)]]... [-allNLength
[(germline|mrca|parent)]]... [-aaLength <gene_feature[,
gene_feature]...> [(germline|mrca|parent)]]... [-allAALength
[(germline|mrca|parent)]]... [-nMutations <gene_feature>
[(germline|mrca|parent)]
[(substitutions|indels|inserts|deletions)]]...
[-allNMutations [(germline|mrca|parent)]
[(substitutions|indels|inserts|deletions)]]...
Expand Down Expand Up @@ -57,8 +60,10 @@ Usage: mixcr exportShmSingleCellTrees [--include-one-chain-trees] [--only-observ
gene_feature]...>]
[(substitutions|indels|inserts|deletions)]]...
[-aaMutationsRate [<gene_feature[,gene_feature]...>]
[(substitutions|indels|inserts|deletions)]]... [-isotype
[(primary|subclass|auto)]]... [-cellId
[(substitutions|indels|inserts|deletions)]]... [-pN
[<gene_feature[,gene_feature]...>]]... [-pS [<gene_feature[,
gene_feature]...>]]... [-pNpS [<gene_feature[,gene_feature]...
>]]... [-isotype [(primary|subclass|auto)]]... [-cellId
[(none|space|dash)]]... [-uniqueTagCount
(Molecule|Cell|Sample)]... [-cellGroup] [-hasStops
<gene_feature>]... [-isOOF <gene_feature>]... [-isProductive
Expand All @@ -84,8 +89,8 @@ separate columns. Initial data for building tree should contain cell data.
--ids <id>[,<id>...] Filter specific trees by id
--chains <chains> Export only trees that contains clones with specific chain (e.g. IGK,
IGL or IGH).
-p, --preset <preset> Specify preset of export fields. Possible values: min, default.
-pf, --preset-file <presetFile>
--preset <preset> Specify preset of export fields. Possible values: min, default.
--preset-file <presetFile>
Specify preset file of export fields
--cell-type <cell_type>...
Export SHM trees for given cell type. By default all will be exported.
Expand Down Expand Up @@ -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 <gene_feature> [(germline|mrca|parent)]
-nFeature <gene_feature> [(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 <gene_feature> [(germline|mrca|parent)]
-aaFeature <gene_feature> [(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`.
Expand Down Expand Up @@ -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 [<gene_feature[,gene_feature]...>]
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 [<gene_feature[,gene_feature]...>]
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 [<gene_feature[,gene_feature]...>]
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`
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4 changes: 2 additions & 2 deletions regression/cli-help/exportShmTrees.txt
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Expand Up @@ -26,9 +26,9 @@ data)
--ids <id>[,<id>...] Filter specific trees by id
--chains <chains> Export only trees that contains clones with specific chain (e.g. IGK,
IGL or IGH).
-p, --preset <preset> Specify preset of export fields. Possible values: default,
--preset <preset> Specify preset of export fields. Possible values: default,
defaultSingleCell, min.
-pf, --preset-file <presetFile>
--preset-file <presetFile>
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.
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64 changes: 42 additions & 22 deletions regression/cli-help/exportShmTreesWithNodes.txt
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Expand Up @@ -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
<gene_feature> [(germline|mrca|parent)]]... [-allNFeatures
[(germline|mrca|parent)]]... [-qFeature <gene_feature>]...
[-allQFeatures [<from_reference_point>
<gene_feature> [(germline|mrca|parent)]
[withAlignmentGaps]]... [-allNFeatures
[(germline|mrca|parent)] [withAlignmentGaps]]... [-qFeature
<gene_feature>]... [-allQFeatures [<from_reference_point>
<to_reference_point>]]... [-aaFeature <gene_feature>
[(germline|mrca|parent)]]... [-allAAFeatures
[(germline|mrca|parent)]]... [-nFeatureImputed <gene_feature>
[(germline|mrca|parent)] [withAlignmentGaps]]...
[-allAAFeatures [(germline|mrca|parent)]
[withAlignmentGaps]]... [-nFeatureImputed <gene_feature>
[(germline|mrca|parent)]]... [-allNFeaturesImputed
[<from_reference_point> <to_reference_point>]
[(germline|mrca|parent)]]... [-aaFeatureImputed <gene_feature>
Expand Down Expand Up @@ -82,17 +84,20 @@ Usage: mixcr exportShmTreesWithNodes [--split-by-tags (Molecule|Cell|Sample)] [-
[-nMutationsRate [<gene_feature[,gene_feature]...>]
[(substitutions|indels|inserts|deletions)]]...
[-aaMutationsRate [<gene_feature[,gene_feature]...>]
[(substitutions|indels|inserts|deletions)]]... [-geneLabel
<label>]... [-isotype [(primary|subclass|auto)]]...
[-tagCounts] [-cellId [(none|space|dash)]]... [-tags
(Molecule|Cell|Sample)]... [-uniqueTagCount
(Molecule|Cell|Sample)]... [-uniqueTagFraction
(Molecule|Cell|Sample)]... [-cellGroup] [-rankByTag
(Molecule|Cell|Sample)]... [-hasStops <gene_feature>]...
[-isOOF <gene_feature>]... [-isProductive [<gene_feature>]]...
[-biochemicalProperty <gene_feature> <property>
[(germline|mrca|parent)]]... [-baseBiochemicalProperties
<gene_feature> [(germline|mrca|parent)]]... [--use-local-temp]
[(substitutions|indels|inserts|deletions)]]... [-pN
[<gene_feature[,gene_feature]...>]]... [-pS [<gene_feature[,
gene_feature]...>]]... [-pNpS [<gene_feature[,gene_feature]...
>]]... [-geneLabel <label>]... [-isotype
[(primary|subclass|auto)]]... [-tagCounts] [-cellId
[(none|space|dash)]]... [-tags (Molecule|Cell|Sample)]...
[-uniqueTagCount (Molecule|Cell|Sample)]...
[-uniqueTagFraction (Molecule|Cell|Sample)]... [-cellGroup]
[-rankByTag (Molecule|Cell|Sample)]... [-hasStops
<gene_feature>]... [-isOOF <gene_feature>]... [-isProductive
[<gene_feature>]]... [-biochemicalProperty <gene_feature>
<property> [(germline|mrca|parent)]]...
[-baseBiochemicalProperties <gene_feature>
[(germline|mrca|parent)]]... [--use-local-temp]
[--force-overwrite] [--no-warnings] [--verbose] [--help]
[[--filter-in-feature <gene_feature>] [--pattern-max-errors
<n>] (--filter-aa-pattern <pattern> | --filter-nt-pattern
Expand All @@ -111,8 +116,8 @@ root if no single cell data)
--ids <id>[,<id>...] Filter specific trees by id
--chains <chains> Export only trees that contains clones with specific chain (e.g. IGK,
IGL or IGH).
-p, --preset <preset> Specify preset of export fields. Possible values: min, default.
-pf, --preset-file <presetFile>
--preset <preset> Specify preset of export fields. Possible values: min, default.
--preset-file <presetFile>
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.
Expand Down Expand Up @@ -211,11 +216,11 @@ Possible fields to export
-dAlignments Export all D alignments (only for nodes with clones)
-jAlignments Export all J alignments (only for nodes with clones)
-cAlignments Export all C alignments (only for nodes with clones)
-nFeature <gene_feature> [(germline|mrca|parent)]
-nFeature <gene_feature> [(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`.
Expand All @@ -229,11 +234,11 @@ Possible fields to export
FR3`, `-qFeature CDR3`, `-qFeature FR4`.
By default, boundaries will be got from analysis parameters if
possible or `FR1Begin FR4End` otherwise. (only for nodes with clones)
-aaFeature <gene_feature> [(germline|mrca|parent)]
-aaFeature <gene_feature> [(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`.
Expand Down Expand Up @@ -471,6 +476,21 @@ 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 [<gene_feature[,gene_feature]...>]
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 [<gene_feature[,gene_feature]...>]
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 [<gene_feature[,gene_feature]...>]
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.
-geneLabel <label> Export gene label (i.e. ReliableChain) (only for nodes with clones)
-isotype [(primary|subclass|auto)]
Export isotype for IGH chains if it's can be distinguishable.
Expand Down

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