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Add a filter for unfiltered 10x MEX data #1511

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Merged
arteymix merged 5 commits into from
Sep 22, 2025
Merged

Add a filter for unfiltered 10x MEX data #1511

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bc752c5
Prototype for filtering 10x MEX data
arteymix Sep 12, 2025
4c929ca
update 10x mex filtering to perform OrdMag and EmptyDrops cell calling
rachadele Sep 20, 2025
60e53d5
make chemistry optional
rachadele Sep 20, 2025
3a4f35b
Cleanup imports in filter-10x-mex.py script
arteymix Sep 21, 2025
ee9b565
Add Rachel to the contributors
arteymix Sep 22, 2025
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8 changes: 4 additions & 4 deletions gemma-cli/src/main/config/bash_completion.d/gemma-cli
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Original file line number Diff line number Diff line change
Expand Up @@ -451,16 +451,16 @@ function __gemma_cli_complete() {
fi
fi
if [[ " $words " =~ ' ubic.gemma.apps.SingleCellDataLoaderCli ' ]]; then
if ! [[ "$current_option" =~ (--anndata-cell-type-factor-name|--anndata-sample-factor-name|--anndata-unknown-cell-type-indicator|--batch-format|--batch-output-file|--batch-report-frequency|--cell-level-characteristics-file|--cell-level-characteristics-name|--cell-type-assignment-description|--cell-type-assignment-file|--cell-type-assignment-name|--cell-type-assignment-protocol|--data-path|--data-type|--eeListfile|--excludeEEFile|--experiment|--experiment-set|--expressionQuery|--fetch-size|--platform|--quantitation-type-name|--quantitation-type-new-name|--quantitation-type-new-scale-type|--quantitation-type-new-type|--quantitation-type-recomputed-from-raw-data|--renaming-file|--sequencing-metadata-file|--sequencing-read-length|--taxon|-a|-annDataCellTypeFactorName|-annDataSampleFactorName|-annDataUnknownCellTypeIndicator|-batchFormat|-batchOutputFile|-batchReportFrequency|-clcFile|-clcName|-ctaDescription|-ctaFile|-ctaName|-ctaProtocol|-dataType|-e|-eeset|-f|-fetchSize|-p|-q|-qtName|-qtNewName|-qtNewScaleType|-qtNewType|-qtRecomputedFromRawData|-renamingFile|-sequencingMetadataFile|-sequencingReadLength|-t|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--anndata-cell-type-factor-name --anndata-ignore-cell-type-factor --anndata-no-transpose --anndata-sample-factor-name --anndata-transpose --anndata-unknown-cell-type-indicator --anndata-use-raw-x --anndata-use-x --batch-format --batch-output-file --batch-report-frequency --cell-level-characteristics-file --cell-level-characteristics-name --cell-type-assignment-description --cell-type-assignment-file --cell-type-assignment-name --cell-type-assignment-protocol --data-path --data-type --eeListfile --excludeEEFile --experiment --experiment-set --expressionQuery --fetch-size --help --ignore-samples-lacking-data --ignore-unmatched-cell-ids --infer-samples-from-cell-ids-overlap --load-cell-level-characteristics --load-cell-type-assignment --load-sequencing-metadata --mex-allow-mapping-design-elements-to-gene-symbols --mex-use-double-precision --no-cursor-fetch --no-streaming --platform --prefer-single-precision --preferred-cell-type-assignment --preferred-quantitation-type --quantitation-type-name --quantitation-type-new-name --quantitation-type-new-scale-type --quantitation-type-new-type --quantitation-type-recomputed-from-raw-data --renaming-file --replace --replace-cell-level-characteristics --replace-cell-type-assignment --sequencing-is-paired --sequencing-is-single-end --sequencing-metadata-file --sequencing-read-length --taxon -a -all -annDataCellTypeFactorName -annDataIgnoreCellTypeFactor -annDataNoTranspose -annDataSampleFactorName -annDataTranspose -annDataUnknownCellTypeIndicator -annDataUseRawX -annDataUseX -batchFormat -batchOutputFile -batchReportFrequency -clcFile -clcName -ctaDescription -ctaFile -ctaName -ctaProtocol -dataType -e -eeset -f -fetchSize -h -ignoreSamplesLackingData -ignoreUnmatchedCellIds -inferSamplesFromCellIdsOverlap -loadClc -loadCta -loadSequencingMetadata -mexAllowMappingDesignElementsToGeneSymbols -mexUseDoublePrecision -noCursorFetch -noStreaming -p -preferSinglePrecision -preferredCta -preferredQt -q -qtName -qtNewName -qtNewScaleType -qtNewType -qtRecomputedFromRawData -renamingFile -replace -replaceClc -replaceCta -sequencingIsPaired -sequencingIsSingleEnd -sequencingMetadataFile -sequencingReadLength -t -x" -- "$2")
if ! [[ "$current_option" =~ (--anndata-cell-type-factor-name|--anndata-sample-factor-name|--anndata-unknown-cell-type-indicator|--batch-format|--batch-output-file|--batch-report-frequency|--cell-level-characteristics-file|--cell-level-characteristics-name|--cell-type-assignment-description|--cell-type-assignment-file|--cell-type-assignment-name|--cell-type-assignment-protocol|--data-path|--data-type|--eeListfile|--excludeEEFile|--experiment|--experiment-set|--expressionQuery|--fetch-size|--mex-10x-chemistry|--platform|--quantitation-type-name|--quantitation-type-new-name|--quantitation-type-new-scale-type|--quantitation-type-new-type|--quantitation-type-recomputed-from-raw-data|--renaming-file|--sequencing-metadata-file|--sequencing-read-length|--taxon|-a|-annDataCellTypeFactorName|-annDataSampleFactorName|-annDataUnknownCellTypeIndicator|-batchFormat|-batchOutputFile|-batchReportFrequency|-clcFile|-clcName|-ctaDescription|-ctaFile|-ctaName|-ctaProtocol|-dataType|-e|-eeset|-f|-fetchSize|-mexChemistry|-p|-q|-qtName|-qtNewName|-qtNewScaleType|-qtNewType|-qtRecomputedFromRawData|-renamingFile|-sequencingMetadataFile|-sequencingReadLength|-t|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--anndata-cell-type-factor-name --anndata-ignore-cell-type-factor --anndata-no-transpose --anndata-sample-factor-name --anndata-transpose --anndata-unknown-cell-type-indicator --anndata-use-raw-x --anndata-use-x --batch-format --batch-output-file --batch-report-frequency --cell-level-characteristics-file --cell-level-characteristics-name --cell-type-assignment-description --cell-type-assignment-file --cell-type-assignment-name --cell-type-assignment-protocol --data-path --data-type --eeListfile --excludeEEFile --experiment --experiment-set --expressionQuery --fetch-size --help --ignore-samples-lacking-data --ignore-unmatched-cell-ids --infer-samples-from-cell-ids-overlap --load-cell-level-characteristics --load-cell-type-assignment --load-sequencing-metadata --mex-10x-chemistry --mex-10x-filter --mex-allow-mapping-design-elements-to-gene-symbols --mex-no-10x-filter --mex-use-double-precision --no-cursor-fetch --no-streaming --platform --prefer-single-precision --preferred-cell-type-assignment --preferred-quantitation-type --quantitation-type-name --quantitation-type-new-name --quantitation-type-new-scale-type --quantitation-type-new-type --quantitation-type-recomputed-from-raw-data --renaming-file --replace --replace-cell-level-characteristics --replace-cell-type-assignment --sequencing-is-paired --sequencing-is-single-end --sequencing-metadata-file --sequencing-read-length --taxon -a -all -annDataCellTypeFactorName -annDataIgnoreCellTypeFactor -annDataNoTranspose -annDataSampleFactorName -annDataTranspose -annDataUnknownCellTypeIndicator -annDataUseRawX -annDataUseX -batchFormat -batchOutputFile -batchReportFrequency -clcFile -clcName -ctaDescription -ctaFile -ctaName -ctaProtocol -dataType -e -eeset -f -fetchSize -h -ignoreSamplesLackingData -ignoreUnmatchedCellIds -inferSamplesFromCellIdsOverlap -loadClc -loadCta -loadSequencingMetadata -mex10xFilter -mexAllowMappingDesignElementsToGeneSymbols -mexChemistry -mexNo10xFilter -mexUseDoublePrecision -noCursorFetch -noStreaming -p -preferSinglePrecision -preferredCta -preferredQt -q -qtName -qtNewName -qtNewScaleType -qtNewType -qtRecomputedFromRawData -renamingFile -replace -replaceClc -replaceCta -sequencingIsPaired -sequencingIsSingleEnd -sequencingMetadataFile -sequencingReadLength -t -x" -- "$2")
fi
if [[ "$current_option" =~ (--batch-output-file|--cell-level-characteristics-file|--cell-type-assignment-file|--data-path|--eeListfile|--excludeEEFile|--renaming-file|--sequencing-metadata-file|-batchOutputFile|-clcFile|-ctaFile|-f|-p|-renamingFile|-sequencingMetadataFile|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
fi
fi
if [[ " $words " =~ ' loadSingleCellData ' ]]; then
if ! [[ "$current_option" =~ (--anndata-cell-type-factor-name|--anndata-sample-factor-name|--anndata-unknown-cell-type-indicator|--batch-format|--batch-output-file|--batch-report-frequency|--cell-level-characteristics-file|--cell-level-characteristics-name|--cell-type-assignment-description|--cell-type-assignment-file|--cell-type-assignment-name|--cell-type-assignment-protocol|--data-path|--data-type|--eeListfile|--excludeEEFile|--experiment|--experiment-set|--expressionQuery|--fetch-size|--platform|--quantitation-type-name|--quantitation-type-new-name|--quantitation-type-new-scale-type|--quantitation-type-new-type|--quantitation-type-recomputed-from-raw-data|--renaming-file|--sequencing-metadata-file|--sequencing-read-length|--taxon|-a|-annDataCellTypeFactorName|-annDataSampleFactorName|-annDataUnknownCellTypeIndicator|-batchFormat|-batchOutputFile|-batchReportFrequency|-clcFile|-clcName|-ctaDescription|-ctaFile|-ctaName|-ctaProtocol|-dataType|-e|-eeset|-f|-fetchSize|-p|-q|-qtName|-qtNewName|-qtNewScaleType|-qtNewType|-qtRecomputedFromRawData|-renamingFile|-sequencingMetadataFile|-sequencingReadLength|-t|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--anndata-cell-type-factor-name --anndata-ignore-cell-type-factor --anndata-no-transpose --anndata-sample-factor-name --anndata-transpose --anndata-unknown-cell-type-indicator --anndata-use-raw-x --anndata-use-x --batch-format --batch-output-file --batch-report-frequency --cell-level-characteristics-file --cell-level-characteristics-name --cell-type-assignment-description --cell-type-assignment-file --cell-type-assignment-name --cell-type-assignment-protocol --data-path --data-type --eeListfile --excludeEEFile --experiment --experiment-set --expressionQuery --fetch-size --help --ignore-samples-lacking-data --ignore-unmatched-cell-ids --infer-samples-from-cell-ids-overlap --load-cell-level-characteristics --load-cell-type-assignment --load-sequencing-metadata --mex-allow-mapping-design-elements-to-gene-symbols --mex-use-double-precision --no-cursor-fetch --no-streaming --platform --prefer-single-precision --preferred-cell-type-assignment --preferred-quantitation-type --quantitation-type-name --quantitation-type-new-name --quantitation-type-new-scale-type --quantitation-type-new-type --quantitation-type-recomputed-from-raw-data --renaming-file --replace --replace-cell-level-characteristics --replace-cell-type-assignment --sequencing-is-paired --sequencing-is-single-end --sequencing-metadata-file --sequencing-read-length --taxon -a -all -annDataCellTypeFactorName -annDataIgnoreCellTypeFactor -annDataNoTranspose -annDataSampleFactorName -annDataTranspose -annDataUnknownCellTypeIndicator -annDataUseRawX -annDataUseX -batchFormat -batchOutputFile -batchReportFrequency -clcFile -clcName -ctaDescription -ctaFile -ctaName -ctaProtocol -dataType -e -eeset -f -fetchSize -h -ignoreSamplesLackingData -ignoreUnmatchedCellIds -inferSamplesFromCellIdsOverlap -loadClc -loadCta -loadSequencingMetadata -mexAllowMappingDesignElementsToGeneSymbols -mexUseDoublePrecision -noCursorFetch -noStreaming -p -preferSinglePrecision -preferredCta -preferredQt -q -qtName -qtNewName -qtNewScaleType -qtNewType -qtRecomputedFromRawData -renamingFile -replace -replaceClc -replaceCta -sequencingIsPaired -sequencingIsSingleEnd -sequencingMetadataFile -sequencingReadLength -t -x" -- "$2")
if ! [[ "$current_option" =~ (--anndata-cell-type-factor-name|--anndata-sample-factor-name|--anndata-unknown-cell-type-indicator|--batch-format|--batch-output-file|--batch-report-frequency|--cell-level-characteristics-file|--cell-level-characteristics-name|--cell-type-assignment-description|--cell-type-assignment-file|--cell-type-assignment-name|--cell-type-assignment-protocol|--data-path|--data-type|--eeListfile|--excludeEEFile|--experiment|--experiment-set|--expressionQuery|--fetch-size|--mex-10x-chemistry|--platform|--quantitation-type-name|--quantitation-type-new-name|--quantitation-type-new-scale-type|--quantitation-type-new-type|--quantitation-type-recomputed-from-raw-data|--renaming-file|--sequencing-metadata-file|--sequencing-read-length|--taxon|-a|-annDataCellTypeFactorName|-annDataSampleFactorName|-annDataUnknownCellTypeIndicator|-batchFormat|-batchOutputFile|-batchReportFrequency|-clcFile|-clcName|-ctaDescription|-ctaFile|-ctaName|-ctaProtocol|-dataType|-e|-eeset|-f|-fetchSize|-mexChemistry|-p|-q|-qtName|-qtNewName|-qtNewScaleType|-qtNewType|-qtRecomputedFromRawData|-renamingFile|-sequencingMetadataFile|-sequencingReadLength|-t|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--anndata-cell-type-factor-name --anndata-ignore-cell-type-factor --anndata-no-transpose --anndata-sample-factor-name --anndata-transpose --anndata-unknown-cell-type-indicator --anndata-use-raw-x --anndata-use-x --batch-format --batch-output-file --batch-report-frequency --cell-level-characteristics-file --cell-level-characteristics-name --cell-type-assignment-description --cell-type-assignment-file --cell-type-assignment-name --cell-type-assignment-protocol --data-path --data-type --eeListfile --excludeEEFile --experiment --experiment-set --expressionQuery --fetch-size --help --ignore-samples-lacking-data --ignore-unmatched-cell-ids --infer-samples-from-cell-ids-overlap --load-cell-level-characteristics --load-cell-type-assignment --load-sequencing-metadata --mex-10x-chemistry --mex-10x-filter --mex-allow-mapping-design-elements-to-gene-symbols --mex-no-10x-filter --mex-use-double-precision --no-cursor-fetch --no-streaming --platform --prefer-single-precision --preferred-cell-type-assignment --preferred-quantitation-type --quantitation-type-name --quantitation-type-new-name --quantitation-type-new-scale-type --quantitation-type-new-type --quantitation-type-recomputed-from-raw-data --renaming-file --replace --replace-cell-level-characteristics --replace-cell-type-assignment --sequencing-is-paired --sequencing-is-single-end --sequencing-metadata-file --sequencing-read-length --taxon -a -all -annDataCellTypeFactorName -annDataIgnoreCellTypeFactor -annDataNoTranspose -annDataSampleFactorName -annDataTranspose -annDataUnknownCellTypeIndicator -annDataUseRawX -annDataUseX -batchFormat -batchOutputFile -batchReportFrequency -clcFile -clcName -ctaDescription -ctaFile -ctaName -ctaProtocol -dataType -e -eeset -f -fetchSize -h -ignoreSamplesLackingData -ignoreUnmatchedCellIds -inferSamplesFromCellIdsOverlap -loadClc -loadCta -loadSequencingMetadata -mex10xFilter -mexAllowMappingDesignElementsToGeneSymbols -mexChemistry -mexNo10xFilter -mexUseDoublePrecision -noCursorFetch -noStreaming -p -preferSinglePrecision -preferredCta -preferredQt -q -qtName -qtNewName -qtNewScaleType -qtNewType -qtRecomputedFromRawData -renamingFile -replace -replaceClc -replaceCta -sequencingIsPaired -sequencingIsSingleEnd -sequencingMetadataFile -sequencingReadLength -t -x" -- "$2")
fi
if [[ "$current_option" =~ (--batch-output-file|--cell-level-characteristics-file|--cell-type-assignment-file|--data-path|--eeListfile|--excludeEEFile|--renaming-file|--sequencing-metadata-file|-batchOutputFile|-clcFile|-ctaFile|-f|-p|-renamingFile|-sequencingMetadataFile|-x) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
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