From 47c8c67d9f2f4f9884fd10e0c497d0c49681e8d0 Mon Sep 17 00:00:00 2001 From: Robert Sheridan Date: Mon, 19 Jul 2021 12:03:12 -0400 Subject: [PATCH] check for new filenames before merge/subset python logic written in separate library - looks for any filenames present in the current datatype sheet (embedded in script) - excludes any filenames which were in use before the introduction of updated filenames - ignore normal sample files (which are ignored by importer) - matches filenames in directory against wildcard patterns (up to a single asterisk) - all filenames of the form *_data_cna_hg18.seg will be allowed (hg18/hg19 and data/meta) - these will not prevent the merge/subset scripts from running (determining cancer_study_id in all cases was not feasible) perform check from subset-impact-data.sh and merge.py and exit on noticing new filename patterns present. --- import-scripts/merge.py | 14 +- ...study_directory_uses_original_filenames.py | 511 ++++++++++++++++++ import-scripts/subset-impact-data.sh | 10 +- .../meta_clinical_patient.txt | 1 + .../meta_clinical_sample.txt | 1 + .../crdb_pdx_raw_data/meta_timeline.txt | 1 + 6 files changed, 536 insertions(+), 2 deletions(-) create mode 100755 import-scripts/study_directory_uses_original_filenames.py diff --git a/import-scripts/merge.py b/import-scripts/merge.py index bfb1c105f..da83374eb 100755 --- a/import-scripts/merge.py +++ b/import-scripts/merge.py @@ -7,6 +7,7 @@ import shutil import re import csv +import study_directory_uses_original_filenames # ------------------------------------------------------------------------------ # globals @@ -103,7 +104,6 @@ 'HYBRIDIZATION REF', ] - # only files fitting patterns placed in these two lists will be merged NORMAL_MERGE_PATTERNS = [MUTATION_META_PATTERN, FUSION_META_PATTERN, @@ -814,6 +814,15 @@ def organize_files(studies, file_types, merge_clinical): else: file_types[SUPP_DATA].append(study_file) +def exit_if_unsupported_filenames_detected(study_paths): + unsupported_filenames_detected = False + for study_path in study_paths: + if not study_directory_uses_original_filenames.study_directory_uses_original_filenames(study_path): + print("unsupported filenames present in study directory '%s' - unable to merge" % study_path) + unsupported_filenames_detected = True + if unsupported_filenames_detected: + sys.exit(2) + def usage(): print >> OUTPUT_FILE, 'merge.py --subset [/path/to/subset] --output-directory [/path/to/output] --study-id [study id] --cancer-type [cancer type] --merge-clinical [true/false] --exclude-supplemental-data [true/false] --excluded-samples [/path/to/exclude_list] ' @@ -919,6 +928,9 @@ def main(): else: exclude_supp_data = True + # test input study paths for new filenames + exit_if_unsupported_filenames_detected(args) + # get all the filenames organize_files(args, file_types, merge_clinical) diff --git a/import-scripts/study_directory_uses_original_filenames.py b/import-scripts/study_directory_uses_original_filenames.py new file mode 100755 index 000000000..bf7d67671 --- /dev/null +++ b/import-scripts/study_directory_uses_original_filenames.py @@ -0,0 +1,511 @@ +#!/usr/bin/env python3 + +import argparse +import os +import sys + +""" +DATATYPE_SHEET_DOWNLOAD_TAB_SEPARATED is hardcoded data - an exact copy of the contents of the current datatypes sheet from the portal_importer_configuration spreadsheet. +When updates are made to the datatypes sheet, this can be updated by using the "File - Download - Tab Separated Values" option in the google sheets interface. +- make sure to copy the exact contents of that download (maintaining the literal TAB characters) into the lines below, between the assignment line and the final triple-quote line +""" +DATATYPE_SHEET_DOWNLOAD_TAB_SEPARATED = """ +datatype DOWNLOAD PROCESS DEPENDENCIES TCGA_DOWNLOAD_ARCHIVE STAGING_FILENAME CONVERTER_CLASSNAME IMPORTER_CLASSNAME REQUIRES_METAFILE META_FILENAME META_STABLE_ID META_GENETIC_ALTERATION_TYPE META_DATATYPE META_SHOW_PROFILE_IN_ANALYSIS_TAB META_PROFILE_NAME META_PROFILE_DESCRIPTION META_REFERENCE_GENOME_ID +bcr-clinical TRUE TRUE nationwidechildrens.org_.bio.Level_2.0..0:nationwidechildrens.org_clinical_patient_.txt;nationwidechildrens.org_.bio.Level_2.0..0:nationwidechildrens.org_clinical_follow_up_v_.txt;nationwidechildrens.org_.bio.Level_2.0..0:nationwidechildrens.org_clinical_nte_.txt;nationwidechildrens.org_.bio.Level_2.0..0:nationwidechildrens.org_clinical_follow_up_v_nte_.txt;nationwidechildrens.org_.bio.Level_2.0..0:nationwidechildrens.org_biospecimen_sample_.txt;nationwidechildrens.org_:nationwidechildrens.org_ data_bcr_clinical_data.txt org.mskcc.cbio.importer.converter.internal.ClinicalDataConverterImpl org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_bcr_clinical.txt bcr_clinical CLINICAL PATIENT_ATTRIBUTES +bcr-clinical-other FALSE FALSE data_bcr_clinical_data_*.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_bcr_clinical_other.txt bcr_clinical_other CLINICAL CLINICAL FALSE Clinical Data Clinical Data +clinical FALSE FALSE data_clinical.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_clinical.txt clinical CLINICAL CLINICAL FALSE Clinical Data Clinical Data +clinical-sample FALSE FALSE data_clinical_sample.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_clinical_sample.txt clinical_sample CLINICAL SAMPLE_ATTRIBUTES FALSE Clinical Data Clinical Data. +clinical-patient FALSE FALSE data_clinical_patient.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_clinical_patient.txt clinical_patient CLINICAL PATIENT_ATTRIBUTES FALSE Clinical Data Clinical Data. +clinical-supp FALSE FALSE data_clinical_supp.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_clinical.txt CLINICAL +clinical-supp-other FALSE FALSE data_clinical_supp_*.txt org.mskcc.cbio.portal.scripts.ImportClinicalData TRUE meta_clinical.txt CLINICAL +clinical-caises FALSE FALSE data_clinical_caises.xml org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML FALSE meta_clinical_caises.txt CLINICAL +time-line-data FALSE FALSE data_timeline.txt org.mskcc.cbio.portal.scripts.ImportTimelineData TRUE meta_timeline.txt CLINICAL +time-line-data-other FALSE FALSE data_timeline_*.txt org.mskcc.cbio.portal.scripts.ImportTimelineData TRUE meta_timeline.txt CLINICAL +rppa TRUE TRUE RPPA_AnnotateWithGene.Level_3:.rppa.txt; data_rppa.txt org.mskcc.cbio.importer.converter.internal.PassThroughConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_rppa.txt rppa PROTEIN_LEVEL LOG2-VALUE FALSE Protein expression (RPPA) Protein expression measured by reverse-phase protein array +rppa-zscores TRUE TRUE rppa RPPA_AnnotateWithGene.Level_3:.rppa.txt; data_rppa_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_rppa_Zscores.txt rppa_Zscores PROTEIN_LEVEL Z-SCORE TRUE Protein expression z-scores (RPPA) Protein expression, measured by reverse-phase protein array, z-scores +protein-quantification FALSE TRUE data_protein_quantification.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_protein_quantification.txt protein_quantification PROTEIN_LEVEL CONTINUOUS FALSE Protein levels (mass spectrometry) Protein levels (mass spectrometry) +protein-quantification-zscores FALSE TRUE protein-quantification data_protein_quantification_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_protein_quantification_Zscores.txt protein_quantification_zscores PROTEIN_LEVEL Z-SCORE TRUE Protein levels z-scores (mass spectrometry) Protein levels z-scores (mass spectrometry) +cna-foundation FALSE TRUE data_CNA_foundation.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_CNA_foundation.txt cna COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from Foundation Putative copy-number calls on cases determined by Foundation Medicine. Values: -2 = homozygous deletion; 2 = high level amplification. +cna-rae FALSE TRUE data_CNA_RAE.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_CNA_RAE.txt cna_rae COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from RAE Putative copy-number calls on cases determined using the RAE algorithm by Barry Taylor @MSKCC. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +cna-consensus FALSE TRUE data_CNA_consensus.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_CNA_consensus.txt cna_consensus COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations (Consensus) Putative copy-number calls for genes which are the consensus of a combination of the Agilent 244k and Affymetrix SNP6 platforms and three different methods (RAE, GISTIC, GTS). +cna-gistic TRUE TRUE CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt; data_CNA.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_CNA.txt gistic COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from GISTIC Putative copy-number calls on cases determined using GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +affymetrix-gene-expression TRUE TRUE Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_expression.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression.txt mrna_U133 MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (U133 microarray only) mRNA expression data from the Affymetrix U133 microarray. +gene-expression-merged TRUE TRUE data_expression_merged.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_merged.txt mrna_U133 MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (U133 microarray only) mRNA expression data from the Affymetrix U133 microarray. +affymetrix-gene-expression-zscores TRUE TRUE cna-gistic:affymetrix-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_expression_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_Zscores.txt mrna_U133_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (U133 microarray only) mRNA z-scores (U133 microarray only) compared to the expression distribution of each gene tumors that are diploid for this gene. +gene-expression-merged-zscores TRUE TRUE cna-gistic:gene-expression-merged CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_expression_merged_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_merged_Zscores.txt mrna_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores mRNA z-scores compared to the expression distribution of each gene tumors that are diploid for this gene. +rnaseq-gene-expression TRUE TRUE Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3:.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt; data_RNA_Seq_expression_median.txt org.mskcc.cbio.importer.converter.internal.RNASEQMRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_median.txt rna_seq_mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq RPKM) Expression levels for genes in cases (RNA Seq RPKM). +rnaseq-gene-expression-zscores TRUE TRUE cna-gistic:rnaseq-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3:.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt; data_RNA_Seq_mRNA_median_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_mRNA_median_Zscores.txt rna_seq_mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (RNA Seq RPKM) mRNA z-scores (RNA Seq RPKM) compared to the expression distribution of each gene tumors that are diploid for this gene. +agilent-gene-expression TRUE TRUE Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt;Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt; data_expression_median.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_median.txt mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (microarray) Expression levels for genes in cases (Agilent microarray). +agilent-gene-expression-zscores TRUE TRUE cna-gistic:agilent-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt;Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt; data_mRNA_median_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_median_Zscores.txt mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (microarray) mRNA z-scores (Agilent microarray) compared to the expression distribution of each gene tumors that are diploid for this gene. +rnaseq-v2-gene-expression TRUE TRUE Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_RNA_Seq_v2_expression_median.txt org.mskcc.cbio.importer.converter.internal.RNASEQV2MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_expression_median.txt rna_seq_v2_mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq V2 RSEM) Expression levels for genes in cases (RNA Seq V2 RSEM). +rnaseq-v2-gene-expression-zscores TRUE TRUE cna-gistic:rnaseq-v2-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_RNA_Seq_v2_mRNA_median_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_mRNA_median_Zscores.txt rna_seq_v2_mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (RNA Seq V2 RSEM) mRNA z-scores (RNA Seq V2 RSEM) compared to the expression distribution of each gene tumors that are diploid for this gene. +rnaseq-gene-expression-cpm FALSE FALSE data_RNA_Seq_expression_cpm.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_cpm.txt mrna_seq_cpm MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq CPM) Expression levels for genes in cases (RNA Seq CPM). +rnaseq-gene-expression-cpm-zscores FALSE FALSE cna-gistic:rnaseq-gene-expression-cpm data_RNA_Seq_expression_cpm_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_cpm_Zscores.txt mrna_seq_cpm_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA expression z-scores (RNA Seq CPM) Expression level z-scores for genes in cases (RNA Seq CPM). +rnaseq-gene-expression-tpm FALSE FALSE data_RNA_Seq_expression_tpm.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_tpm.txt mrna_seq_tpm MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq TPM) Expression levels for genes in cases (RNA Seq TPM). +rnaseq-gene-expression-tpm-zscores FALSE FALSE cna-gistic:rnaseq-gene-expression-tpm data_RNA_Seq_expression_tpm_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_tpm_Zscores.txt mrna_seq_tpm_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA expression z-scores (RNA Seq TPM) Expression level z-scores for genes in cases (RNA Seq TPM). +cna-hg19-seg TRUE TRUE Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3:.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt; _data_cna_hg19.seg org.mskcc.cbio.importer.converter.internal.CopyNumberSegmentConverterImpl org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData TRUE _meta_cna_hg19_seg.txt COPY_NUMBER_ALTERATION SEG Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA. hg19 +cna-hg18-seg TRUE TRUE Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.Level_3:.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt; _data_cna_hg18.seg org.mskcc.cbio.importer.converter.internal.CopyNumberSegmentConverterImpl org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData TRUE _meta_cna_hg18_seg.txt COPY_NUMBER_ALTERATION SEG Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA. hg18 +cna-hg19-seg-std TRUE TRUE Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3:.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt; data_cna_hg19.seg org.mskcc.cbio.importer.converter.internal.CopyNumberSegmentConverterImpl org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData TRUE meta_cna_hg19_seg.txt COPY_NUMBER_ALTERATION SEG Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA. hg19 +cna-hg18-seg-std TRUE TRUE Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.Level_3:.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt; data_cna_hg18.seg org.mskcc.cbio.importer.converter.internal.CopyNumberSegmentConverterImpl org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData TRUE meta_cna_hg18_seg.txt COPY_NUMBER_ALTERATION SEG Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA. hg18 +gistic-genes-amp TRUE TRUE CopyNumber_Gistic2.Level_4:amp_genes.conf_99.txt;CopyNumber_Gistic2.Level_4:table_amp.conf_99.txt; data_gistic_genes_amp.txt org.mskcc.cbio.importer.converter.internal.GisticGenesConverterImpl org.mskcc.cbio.portal.scripts.ImportGisticData FALSE meta_gistic_genes_amp.txt gistic_genes_amp GISTIC_GENES_AMP Q-VALUE FALSE Putative copy-number alterations (amplifications) from GISTIC Putative copy-number amplifications determined using GISTIC 2.0. hg19 +gistic-genes-del TRUE TRUE CopyNumber_Gistic2.Level_4:del_genes.conf_99.txt;CopyNumber_Gistic2.Level_4:table_del.conf_99.txt; data_gistic_genes_del.txt org.mskcc.cbio.importer.converter.internal.GisticGenesConverterImpl org.mskcc.cbio.portal.scripts.ImportGisticData FALSE meta_gistic_genes_del.txt gistic_genes_del GISTIC_GENES_DEL Q-VALUE FALSE Putative copy-number alterations (deletions) from GISTIC Putative copy-number deletions determined using GISTIC 2.0. hg19 +linear-cna-gistic TRUE TRUE CopyNumber_Gistic2.Level_4:all_data_by_genes.txt; data_linear_CNA.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_linear_CNA.txt linear_CNA COPY_NUMBER_ALTERATION CONTINUOUS FALSE Relative linear copy-number values Relative linear copy-number values for each gene (from Affymetrix SNP6). +log2-cna TRUE TRUE data_log2CNA.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_log2CNA.txt log2CNA COPY_NUMBER_ALTERATION LOG2-VALUE FALSE Log2 copy-number values Log2 copy-number values for each gene. +armlevel_cna FALSE FALSE data_armlevel_CNA.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_armlevel_CNA.txt armlevel_cna GENERIC_ASSAY CATEGORICAL TRUE Putative arm-level copy-number from GISTIC Putative arm-level copy-number from GISTIC 2.0. +methylation-hm27 TRUE TRUE Correlate_Methylation_vs_mRNA.Level_4:Correlate_Methylation_vs_mRNA__matrix.txt;Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3:.methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt; data_methylation_hm27.txt org.mskcc.cbio.importer.converter.internal.MethylationConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_hm27.txt methylation_hm27 METHYLATION CONTINUOUS FALSE Methylation (HM27) Methylation (HM27) beta-values for genes in cases. For genes with multiple methylation probes, the probe most anti-correlated with expression. +methylation-hm450 TRUE TRUE Correlate_Methylation_vs_mRNA.Level_4:Correlate_Methylation_vs_mRNA__matrix.txt;Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3:.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt; data_methylation_hm450.txt org.mskcc.cbio.importer.converter.internal.MethylationConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_hm450.txt methylation_hm450 METHYLATION CONTINUOUS FALSE Methylation (HM450) Methylation (HM450) beta-values for genes in cases. For genes with multiple methylation probes, the probe most anti-correlated with expression. +methylation-promoters-hmepic TRUE TRUE data_methylation_promoters_hmEPIC.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_promoters_hmEPIC.txt methylation_promoters_hmEPIC METHYLATION CONTINUOUS TRUE Methylation (HMEPIC) Methylation beta-values (Infinium MethylationEPIC platform). This matrix is collapsed to include only promoters. +methylation-promoters-wgbs TRUE TRUE data_methylation_promoters_wgbs.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_promoters_wgbs.txt methylation_promoters_wgbs METHYLATION CONTINUOUS TRUE Methylation (WGBS) Methylation beta-values by whole-genome bisulfite sequencing. Values are the average fractional methylation value across promoter CpGs for the labeled gene. +methylation-genebodies-hmepic TRUE TRUE data_methylation_genebodies_hmEPIC.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_genebodies_hmEPIC.txt methylation_genebodies_hmEPIC METHYLATION CONTINUOUS TRUE Methylation (HMEPIC) Methylation beta-values (HMEPIC platform). Values are the average fractional methylation value across exons for the labeled gene. +methylation-genebodies-wgbs TRUE TRUE data_methylation_genebodies_wgbs.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_genebodies_wgbs.txt methylation_genebodies_wgbs METHYLATION CONTINUOUS TRUE Methylation (WGBS) Methylation beta-values by whole-genome bisulfite sequencing. Values are the average fractional methylation value across exons of the labeled gene. +mutation-foundation FALSE FALSE data_mutations_extended_foundation.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations from Foundation Putative mutation calls on cases determined by Foundation Medicine. +mutation TRUE TRUE Mutation_Packager_Calls.Level_3:.maf.txt;Mutation_Packager_Raw_Calls.Level_3:.maf.txt data_mutations_extended.txt org.mskcc.cbio.importer.converter.internal.MutationConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation-other FALSE TRUE data_mutations_extended_*.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation_germline FALSE FALSE data_mutations_germline.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation_nonsignedout FALSE FALSE data_mutations_nonsignedout.txt TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation-uncalled FALSE FALSE data_mutations_uncalled.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_uncalled.txt mutations_uncalled MUTATION_UNCALLED MAF FALSE Mutations Uncalled Mutation data from whole exome sequencing. (Uncalled) +mutation-manual FALSE TRUE data_mutations_manual.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_extended.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data that are manually curated. +gene-panel FALSE TRUE data_gene_panel.txt org.mskcc.cbio.portal.scripts.ImportGenePanel FALSE +gene-panel FALSE TRUE data_gene_panel_*.txt org.mskcc.cbio.portal.scripts.ImportGenePanel FALSE +mutation-significance-v2 TRUE TRUE MutSigNozzleReport2.0.Level_4:.sig_genes.txt; data_mutsig.txt org.mskcc.cbio.importer.converter.internal.PassThroughConverterImpl org.mskcc.cbio.portal.scripts.ImportMutSigData FALSE meta_mutsig.txt mutsig MUTSIG Q-VALUE FALSE Mutation analysis via MutSig from whole exome sequencing. +fusion FALSE FALSE data_fusions.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_fusions.txt mutations FUSION FUSION FALSE Fusions Fusion data derived from mutation file. +mirna-expression TRUE TRUE miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt data_expression_miRNA.txt org.mskcc.cbio.importer.converter.internal.MIRNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_miRNA.txt mirna MRNA_EXPRESSION CONTINUOUS FALSE microRNA expression Expression levels for microRNAs. +mirna-median-zscores FALSE TRUE miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt data_miRNA_median_Zscores.txt org.mskcc.cbio.importer.converter.internal.MIRNAZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_miRNA_median_Zscores.txt mirna_median_Zscores MRNA_EXPRESSION Z-SCORE FALSE microRNA expression z-scores microRNA expression z-scores compared to all tumors. +mirna-merged-median-zscores FALSE TRUE mirna-median-zscores:rnaseq-v2-gene-expression miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt;Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_expression_merged_median_Zscores.txt org.mskcc.cbio.importer.converter.internal.MIRNAMergedMedianZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_merged_median_Zscores.txt mrna_merged_median_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA/miRNA expression z-scores (all genes) mRNA and microRNA z-scores merged: mRNA expression z-scores compared to diploid tumors (diploid for each gene), median values from all three mRNA expression platforms; and miRNA z-scores compared to all tumours. +mrna-outliers FALSE TRUE data_mRNA_outliers.txt org.mskcc.cbio.importer.converter.internal.PassThroughConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_outliers.txt mrna_outliers MRNA_EXPRESSION DISCRETE FALSE mRNA Expression Outliers mRNA expression outliers compared to normals (-1 = underexpressed, 1 = overexpressed). +capture-gene-expression FALSE FALSE data_RNA_Seq_expression_capture.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_capture.txt rna_seq_mrna_capture MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression / capture (RNA Seq capture) mRNA expression from capture (RNA Seq RPKM) +capture-gene-expression-zscores FALSE FALSE cna-gistic:capture-gene-expression data_RNA_Seq_expression_capture_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_capture_Zscores.txt rna_seq_mrna_capture_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression / capture z-scores (RNA Seq capture) mRNA expression from capture z-scores (RNA Seq RPKM) +other-gene-expression-zscores FALSE FALSE data_expression_other_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_other_Zscores.txt +methylation-binary FALSE FALSE data_methylation_binary.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_methylation_binary.txt +mrna-seq-fpkm FALSE FALSE data_mRNA_seq_fpkm.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm.txt mrna_seq_fpkm MRNA_EXPRESSION CONTINUOUS mRNA expression (FPKM) mRNA expression from capture (RNA Seq FPKM) +mrna-seq-rsem data_mrnaseq_rsem.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrnaseq_rsem.txt +mrna-seq-fcount data_mrnaseq_fcount.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrnaseq_fcount.txt +mrna-seq-fpkm-capture FALSE FALSE data_mRNA_seq_fpkm_capture.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_capture.txt mrna_seq_fpkm_capture MRNA_EXPRESSION CONTINUOUS mRNA expression (FPKM capture) mRNA expression from capture (RNA Seq FPKM) +mrna-seq-fpkm-polya FALSE FALSE data_mRNA_seq_fpkm_polya.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_polya.txt mrna_seq_fpkm_polya MRNA_EXPRESSION CONTINUOUS mRNA expression (FPKM polyA) mRNA expression from polyA (RNA Seq FPKM) +mrna-seq-fpkm-capture-zscores FALSE FALSE cna-gistic:mrna-seq-fpkm-capture data_mRNA_seq_fpkm_capture_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_capture_Zscores.txt mrna_seq_fpkm_capture_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (FPKM capture) mRNA expression from capture z-scores (RNA Seq FPKM) +mrna-seq-fpkm-polya-zscores FALSE FALSE cna-gistic:mrna-seq-fpkm-polya data_mRNA_seq_fpkm_polya_Zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_polya_Zscores.txt mrna_seq_fpkm_polya_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (FPKM polyA) mRNA expression from polyA z-scores (RNA Seq FPKM) +fusion-gml FALSE FALSE data_fusions_gml.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_fusions_gml.txt mutations FUSION FUSION_GML FALSE Fusions (GML) Fusion data derived from mutation file. (GML) +gsva-scores FALSE TRUE data_gsva_scores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_gsva_scores.txt gsva_scores GENESET_SCORE GSVA-SCORE FALSE GSVA scores +gsva-pvalues FALSE TRUE data_gsva_pvalues.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_gsva_pvalues.txt gsva_pvalues GENESET_SCORE P-VALUE FALSE GSVA p-values +drug-treatment-ic50 data_drug_treatment_IC50.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_IC50.txt CCLE_drug_treatment_IC50 GENERIC_ASSAY LIMIT-VALUE TRUE Treatment response: IC50 Treatment response: IC50 +drug-treatment-ic50-zscores data_drug_treatment_ZSCORE.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_ZSCORE.txt CCLE_drug_treatment_zscore GENERIC_ASSAY LIMIT-VALUE TRUE Treament response: z-score of IC50 Treament response: z-score of IC50 +drug-treatment-auc data_drug_treatment_AUC.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_AUC.txt CCLE_drug_treatment_AUC GENERIC_ASSAY LIMIT-VALUE TRUE Treatment response: AUC Treatment response: AUC +rnaseq-v2-gene-expression-all-sample-zscores FALSE FALSE rnaseq-v2-gene-expression data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt rna_seq_v2_mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq V2 RSEM). +agilent-gene-expression-all-sample-zscores FALSE FALSE agilent-gene-expression data_mRNA_median_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_median_all_sample_Zscores.txt mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log microarray) Log-transformed mRNA z-scores compared to the expression distribution of all samples (Agilent microarray). +affymetrix-gene-expression-all-sample-zscores FALSE FALSE affymetrix-gene-expression data_expression_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_expression_all_sample_Zscores.txt mrna_U133_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log U133 microarray only) Log-transformed mRNA z-scores compared to the expression distribution of all samples (U133 microarray only). +rnaseq-gene-expression-all-sample-zscores FALSE FALSE rnaseq-gene-expression data_RNA_Seq_mRNA_median_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_mRNA_median_all_sample_Zscores.txt rna_seq_mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq RPKM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq RPKM). +rnaseq-gene-expression-cpm-all-sample-zscores FALSE FALSE rnaseq-gene-expression-cpm data_RNA_Seq_expression_cpm_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_cpm_all_sample_Zscores.txt mrna_seq_cpm_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq CPM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq CPM). +rnaseq-gene-expression-tpm-all-sample-zscores FALSE FALSE rnaseq-gene-expression-tpm data_RNA_Seq_expression_tpm_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_tpm_all_sample_Zscores.txt mrna_seq_tpm_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq TPM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq TPM). +capture-gene-expression-all-sample-zscores FALSE FALSE capture-gene-expression data_RNA_Seq_expression_capture_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_expression_capture_all_sample_Zscores.txt rna_seq_mrna_capture_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression / capture z-scores relative to all samples (log RNA Seq capture) Log-transformed mRNA z-scores compared to the expression distribution across all samples (RNA Seq RPKM capture) +mrna-seq-fpkm-capture-all-sample-zscores FALSE FALSE mrna-seq-fpkm-capture data_mRNA_seq_fpkm_capture_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_capture_all_sample_Zscores.txt mrna_seq_fpkm_capture_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log FPKM capture) Log-transformed mRNA z-scores compared to expression distribution of all samples (RNA Seq FPKM capture) +mrna-seq-fpkm-polya-all-sample-zscores FALSE FALSE mrna-seq-fpkm-polya data_mRNA_seq_fpkm_polya_all_sample_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mRNA_seq_fpkm_polya_all_sample_Zscores.txt mrna_seq_fpkm_polya_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log FPKM polyA) Log-transformed mRNA z-scores compared to expression distribution of all samples (RNA Seq FPKM polyA) +microbiome-signatures FALSE FALSE data_microbiome.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_microbiome.txt microbiome_signature GENERIC_ASSAY LIMIT-VALUE TRUE Cancer Microbiome Data (log2-CPM Normalized) Microbial Signatures (log-cpm) from whole genome and whole-transcriptome sequencing studies of TCGA. +rnaseq-v2-gene-expression-normal FALSE FALSE data_RNA_Seq_v2_mRNA_median_normals.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_mRNA_median_normals.txt rna_seq_v2_mrna_median_normals MRNA_EXPRESSION CONTINUOUS TRUE mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) +rnaseq-v2-gene-expression-normal-zscores FALSE FALSE data_RNA_Seq_v2_mRNA_median_Zscores_normals.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_mRNA_median_Zscores_normals.txt rna_seq_v2_mrna_median_normals_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression of adjacent normal samples, z-scores relative to all normal samples (log RNA Seq V2 RSEM) Expression z-scores of adjacent normal samples compared to the expression distribution of all log-transformed mRNA expression of adjacent normal samples in the cohort. +rnaseq-v2-gene-expression-all-sample-ref-normal-zscores FALSE FALSE data_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to normal samples (log RNA Seq V2 RSEM) Expression z-scores of tumor samples compared to the expression distribution of all log-transformed mRNA expression of adjacent normal samples in the cohort. +mutational-signature-contribution-v2 FALSE FALSE data_mutational_signature_contribution_v2.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutational_signature_contribution_v2.txt mutational_signature_contribution_v2 GENERIC_ASSAY LIMIT-VALUE TRUE mutational signature contribution v2 profile for contribution value of mutational signatures (COSMIC version 2) +mutational-signature-pvalue-v2 FALSE FALSE data_mutational_signature_pvalue_v2.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutational_signature_pvalue_v2.txt mutational_signature_pvalue_v2 GENERIC_ASSAY LIMIT-VALUE FALSE mutational signature pvalue v2 profile for pvalue of mutational signatures (COSMIC version 2) +mutational-signature-contribution-v3 FALSE FALSE data_mutational_signature_contribution_v3.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutational_signature_contribution_v3.txt mutational_signature_contribution_v3 GENERIC_ASSAY LIMIT-VALUE TRUE mutational signature contribution v3 profile for contribution value of mutational signatures (COSMIC version 3) +mutational-signature-pvalue-v3 FALSE FALSE data_mutational_signature_pvalue_v3.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutational_signature_pvalue_v3.txt mutational_signature_pvalue_v3 GENERIC_ASSAY LIMIT-VALUE FALSE mutational signature pvalue v3 profile for pvalue of mutational signatures (COSMIC version 3) +resource-definition FALSE data_resource_definition.txt org.mskcc.cbio.portal.scripts.ImportResourceDefinition TRUE meta_resource_definition.txt +resource-study FALSE data_resource_study.txt org.mskcc.cbio.portal.scripts.ImportResourceData TRUE meta_resource_study.txt +resource-sample FALSE data_resource_sample.txt org.mskcc.cbio.portal.scripts.ImportResourceData TRUE meta_resource_sample.txt +phosphoprotein_quantification FALSE data_phosphoprotein_quantification.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_phosphoprotein_quantification.txt phosphoprotein_quantification GENERIC_ASSAY LIMIT-VALUE TRUE Phosphoprotein site level expression data by CPTAC (TMT, Log2ratio) Phosphoprotein site level expression data given in log-ratio (normalized) by CPTAC. +mirna-expression TRUE TRUE miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt data_mirna.txt org.mskcc.cbio.importer.converter.internal.MIRNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mirna.txt mirna MRNA_EXPRESSION CONTINUOUS FALSE microRNA expression Expression levels for microRNAs. +mirna-median-zscores FALSE TRUE miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt data_mirna_zscores.txt org.mskcc.cbio.importer.converter.internal.MIRNAZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mirna_zscores.txt mirna_median_Zscores MRNA_EXPRESSION Z-SCORE FALSE microRNA expression z-scores microRNA expression z-scores compared to all tumors. +affymetrix-gene-expression TRUE TRUE Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_mrna_affymetrix_microarray.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_affymetrix_microarray.txt mrna_U133 MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (U133 microarray only) mRNA expression data from the Affymetrix U133 microarray. +affymetrix-gene-expression-zscores TRUE TRUE cna-gistic:affymetrix-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt mrna_U133_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (U133 microarray only) mRNA z-scores (U133 microarray only) compared to the expression distribution of each gene tumors that are diploid for this gene. +affymetrix-gene-expression-all-sample-zscores FALSE FALSE affymetrix-gene-expression data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_affymetrix_microarray_zscores_ref_all_samples.txt mrna_U133_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log U133 microarray only) Log-transformed mRNA z-scores compared to the expression distribution of all samples (U133 microarray only). +agilent-gene-expression TRUE TRUE Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt;Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt; data_mrna_agilent_microarray.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_agilent_microarray.txt mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (microarray) Expression levels for genes in cases (Agilent microarray). +agilent-gene-expression-zscores TRUE TRUE cna-gistic:agilent-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt;Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3:.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt; data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_agilent_microarray_zscores_ref_diploid_samples.txt mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (microarray) mRNA z-scores (Agilent microarray) compared to the expression distribution of each gene tumors that are diploid for this gene. +agilent-gene-expression-all-sample-zscores FALSE FALSE agilent-gene-expression data_mrna_agilent_microarray_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_agilent_microarray_zscores_ref_all_samples.txt mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log microarray) Log-transformed mRNA z-scores compared to the expression distribution of all samples (Agilent microarray). +rnaseq-gene-expression TRUE TRUE Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3:.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt; data_mrna_seq_rpkm.txt org.mskcc.cbio.importer.converter.internal.RNASEQMRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_rpkm.txt rna_seq_mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq RPKM) Expression levels for genes in cases (RNA Seq RPKM). +rnaseq-gene-expression-zscores TRUE TRUE cna-gistic:rnaseq-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.Level_3:.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__gene_expression__data.data.txt; data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_rpkm_zscores_ref_diploid_samples.txt rna_seq_mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (RNA Seq RPKM) mRNA z-scores (RNA Seq RPKM) compared to the expression distribution of each gene tumors that are diploid for this gene. +rnaseq-gene-expression-all-sample-zscores FALSE FALSE rnaseq-gene-expression data_mrna_seq_rpkm_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_rpkm_zscores_ref_all_samples.txt rna_seq_mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq RPKM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq RPKM). +rnaseq-v2-gene-expression TRUE TRUE Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_mrna_seq_v2_rsem.txt org.mskcc.cbio.importer.converter.internal.RNASEQV2MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem.txt rna_seq_v2_mrna MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq V2 RSEM) Expression levels for genes in cases (RNA Seq V2 RSEM). +rnaseq-v2-gene-expression-zscores TRUE TRUE cna-gistic:rnaseq-v2-gene-expression CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt rna_seq_v2_mrna_median_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (RNA Seq V2 RSEM) mRNA z-scores (RNA Seq V2 RSEM) compared to the expression distribution of each gene tumors that are diploid for this gene. +rnaseq-v2-gene-expression-all-sample-zscores FALSE FALSE rnaseq-v2-gene-expression data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem_zscores_ref_all_samples.txt rna_seq_v2_mrna_median_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq V2 RSEM). +rnaseq-v2-gene-expression-normal FALSE FALSE data_mrna_seq_v2_rsem_normal_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem_normal_samples.txt rna_seq_v2_mrna_median_normals MRNA_EXPRESSION CONTINUOUS TRUE mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2) +rnaseq-v2-gene-expression-normal-zscores FALSE FALSE data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt rna_seq_v2_mrna_median_normals_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression of adjacent normal samples, z-scores relative to all normal samples (log RNA Seq V2 RSEM) Expression z-scores of adjacent normal samples compared to the expression distribution of all log-transformed mRNA expression of adjacent normal samples in the cohort. +rnaseq-v2-gene-expression-all-sample-ref-normal-zscores FALSE FALSE data_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to normal samples (log RNA Seq V2 RSEM) Expression z-scores of tumor samples compared to the expression distribution of all log-transformed mRNA expression of adjacent normal samples in the cohort. +rnaseq-gene-expression-cpm FALSE FALSE data_mrna_seq_cpm.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_cpm.txt mrna_seq_cpm MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq CPM) Expression levels for genes in cases (RNA Seq CPM). +rnaseq-gene-expression-cpm-zscores FALSE FALSE cna-gistic:rnaseq-gene-expression-cpm data_mrna_seq_cpm_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_cpm_zscores_ref_diploid_samples.txt mrna_seq_cpm_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA expression z-scores (RNA Seq CPM) Expression level z-scores for genes in cases (RNA Seq CPM). +rnaseq-gene-expression-cpm-all-sample-zscores FALSE FALSE rnaseq-gene-expression-cpm data_mrna_seq_cpm_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_cpm_zscores_ref_all_samples.txt mrna_seq_cpm_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq CPM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq CPM). +rnaseq-gene-expression-tpm FALSE FALSE data_mrna_seq_tpm.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_tpm.txt mrna_seq_tpm MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (RNA Seq TPM) Expression levels for genes in cases (RNA Seq TPM). +rnaseq-gene-expression-tpm-zscores FALSE FALSE cna-gistic:rnaseq-gene-expression-tpm data_mrna_seq_tpm_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_tpm_zscores_ref_diploid_samples.txt mrna_seq_tpm_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA expression z-scores (RNA Seq TPM) Expression level z-scores for genes in cases (RNA Seq TPM). +rnaseq-gene-expression-tpm-all-sample-zscores FALSE FALSE rnaseq-gene-expression-tpm data_mrna_seq_tpm_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_tpm_zscores_ref_all_samples.txt mrna_seq_tpm_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log RNA Seq TPM) Log-transformed mRNA z-scores compared to the expression distribution of all samples (RNA Seq TPM). +mrna-seq-fpkm-capture FALSE FALSE data_mrna_seq_fpkm_capture.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_capture.txt mrna_seq_fpkm_capture MRNA_EXPRESSION CONTINUOUS mRNA expression (FPKM capture) mRNA expression from capture (RNA Seq FPKM) +mrna-seq-fpkm-capture-zscores FALSE FALSE cna-gistic:mrna-seq-fpkm-capture data_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt mrna_seq_fpkm_capture_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (FPKM capture) mRNA expression from capture z-scores (RNA Seq FPKM) +mrna-seq-fpkm-capture-all-sample-zscores FALSE FALSE mrna-seq-fpkm-capture data_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt mrna_seq_fpkm_capture_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log FPKM capture) Log-transformed mRNA z-scores compared to expression distribution of all samples (RNA Seq FPKM capture) +mrna-seq-fpkm-polya FALSE FALSE data_mrna_seq_fpkm_polya.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_polya.txt mrna_seq_fpkm_polya MRNA_EXPRESSION CONTINUOUS mRNA expression (FPKM polyA) mRNA expression from polyA (RNA Seq FPKM) +mrna-seq-fpkm-polya-zscores FALSE FALSE cna-gistic:mrna-seq-fpkm-polya data_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt mrna_seq_fpkm_polya_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores (FPKM polyA) mRNA expression from polyA z-scores (RNA Seq FPKM) +mrna-seq-fpkm-polya-all-sample-zscores FALSE FALSE mrna-seq-fpkm-polya data_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt mrna_seq_fpkm_polya_all_sample_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores relative to all samples (log FPKM polyA) Log-transformed mRNA z-scores compared to expression distribution of all samples (RNA Seq FPKM polyA) +mirna-merged-median-zscores FALSE TRUE mirna-median-zscores:rnaseq-v2-gene-expression miRseq_Mature_Preprocess.Level_3:.miRseq_mature_RPM.txt;Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3:.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt; data_mrna_mirna_merged_zscores.txt org.mskcc.cbio.importer.converter.internal.MIRNAMergedMedianZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_mirna_merged_zscores.txt mrna_merged_median_Zscores MRNA_EXPRESSION Z-SCORE FALSE mRNA/miRNA expression z-scores (all genes) mRNA and microRNA z-scores merged: mRNA expression z-scores compared to diploid tumors (diploid for each gene), median values from all three mRNA expression platforms; and miRNA z-scores compared to all tumours. +gene-expression-merged TRUE TRUE data_mrna_affymetrix_microarray_merged.txt org.mskcc.cbio.importer.converter.internal.MRNAMedianConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_affymetrix_microarray_merged.txt mrna_U133 MRNA_EXPRESSION CONTINUOUS FALSE mRNA expression (U133 microarray only) mRNA expression data from the Affymetrix U133 microarray. +gene-expression-merged-zscores TRUE TRUE cna-gistic:gene-expression-merged CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt;Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3:.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt data_mrna_affymetrix_microarray_merged_zscores_ref_diploid_samples.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_affymetrix_microarray_merged_zscores_ref_diploid_samples.txt mrna_Zscores MRNA_EXPRESSION Z-SCORE TRUE mRNA expression z-scores mRNA z-scores compared to the expression distribution of each gene tumors that are diploid for this gene. +mrna-outliers FALSE TRUE data_mrna_outliers.txt org.mskcc.cbio.importer.converter.internal.PassThroughConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mrna_outliers.txt mrna_outliers MRNA_EXPRESSION DISCRETE FALSE mRNA Expression Outliers mRNA expression outliers compared to normals (-1 = underexpressed, 1 = overexpressed). +rppa-zscores TRUE TRUE rppa RPPA_AnnotateWithGene.Level_3:.rppa.txt; data_rppa_zscores.txt org.mskcc.cbio.importer.converter.internal.ZScoresConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_rppa_zscores.txt rppa_Zscores PROTEIN_LEVEL Z-SCORE TRUE Protein expression z-scores (RPPA) Protein expression, measured by reverse-phase protein array, z-scores +protein-quantification-zscores FALSE TRUE protein-quantification data_protein_quantification_zscores.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_protein_quantification_zscores.txt protein_quantification_zscores PROTEIN_LEVEL Z-SCORE TRUE Protein levels z-scores (mass spectrometry) Protein levels z-scores (mass spectrometry) +cna-foundation FALSE TRUE data_cna_foundation.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_cna_foundation.txt cna COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from Foundation Putative copy-number calls on cases determined by Foundation Medicine. Values: -2 = homozygous deletion; 2 = high level amplification. +cna-rae FALSE TRUE data_cna_rae.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_cna_rae.txt cna_rae COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from RAE Putative copy-number calls on cases determined using the RAE algorithm by Barry Taylor @MSKCC. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +cna-consensus FALSE TRUE data_cna_consensus.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_cna_consensus.txt cna_consensus COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations (Consensus) Putative copy-number calls for genes which are the consensus of a combination of the Agilent 244k and Affymetrix SNP6 platforms and three different methods (RAE, GISTIC, GTS). +cna-gistic TRUE TRUE CopyNumber_Gistic2.Level_4:all_thresholded.by_genes.txt; data_cna.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_cna.txt gistic COPY_NUMBER_ALTERATION DISCRETE TRUE Putative copy-number alterations from GISTIC Putative copy-number calls on cases determined using GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +linear-cna-gistic TRUE TRUE CopyNumber_Gistic2.Level_4:all_data_by_genes.txt; data_linear_cna.txt org.mskcc.cbio.importer.converter.internal.CNAConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_linear_cna.txt linear_CNA COPY_NUMBER_ALTERATION CONTINUOUS FALSE Relative linear copy-number values Relative linear copy-number values for each gene (from Affymetrix SNP6). +log2-cna TRUE TRUE data_log2_cna.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_log2_cna.txt log2CNA COPY_NUMBER_ALTERATION LOG2-VALUE FALSE Log2 copy-number values Log2 copy-number values for each gene. +armlevel_cna FALSE FALSE data_armlevel_cna.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_armlevel_cna.txt armlevel_cna GENERIC_ASSAY CATEGORICAL TRUE Putative arm-level copy-number from GISTIC Putative arm-level copy-number from GISTIC 2.0. +drug-treatment-auc data_drug_treatment_auc.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_auc.txt CCLE_drug_treatment_AUC GENERIC_ASSAY LIMIT-VALUE TRUE Treatment response: AUC Treatment response: AUC +drug-treatment-ic50 data_drug_treatment_ic50.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_ic50.txt CCLE_drug_treatment_IC50 GENERIC_ASSAY LIMIT-VALUE TRUE Treatment response: IC50 Treatment response: IC50 +drug-treatment-ic50-zscores data_drug_treatment_zscore.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_drug_treatment_zscore.txt CCLE_drug_treatment_zscore GENERIC_ASSAY LIMIT-VALUE TRUE Treament response: z-score of IC50 Treament response: z-score of IC50 +mutation TRUE TRUE Mutation_Packager_Calls.Level_3:.maf.txt;Mutation_Packager_Raw_Calls.Level_3:.maf.txt data_mutations_uniprot_canonical_transcripts.txt org.mskcc.cbio.importer.converter.internal.MutationConverterImpl org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_uniprot_canonical_transcripts.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation-other FALSE TRUE data_mutations_uniprot_canonical_transcripts_*.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_uniprot_canonical_transcripts.txt mutations MUTATION_EXTENDED MAF TRUE Mutations Mutation data from whole exome sequencing. +mutation-foundation FALSE FALSE data_mutations_uniprot_canonical_transcripts_foundation.txt org.mskcc.cbio.portal.scripts.ImportProfileData TRUE meta_mutations_uniprot_canonical_transcripts.txt +gene-panel-matrix FALSE TRUE data_gene_matrix.txt org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap TRUE meta_gene_matrix.txt +gene-panel-matrix FALSE TRUE data_gene_panel_matrix.txt org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap TRUE meta_gene_panel_matrix.txt +""" + +""" +FILENAMES_IN_USE_BEFORE_UPDATE_LIST is a hardcoded list of old filenames which were recognized before the file renaming effort of mid-2021. +The merge.py and subset-dmp-data.sh scripts were working with studies limited to these filenames. +We have decided to allow running of the merge/subset scripts regardless of whether the prefix on seg file filenames matches the cancer study. Determining the actual cancer study in all use cases was not feasible. +""" +FILENAMES_IN_USE_BEFORE_UPDATE_LIST = [ + "*_data_cna_hg18.seg", + "*_data_cna_hg19.seg", + "*_meta_cna_hg18_seg.txt", + "*_meta_cna_hg19_seg.txt", + "data_CNA.txt", + "data_CNA_RAE.txt", + "data_CNA_consensus.txt", + "data_CNA_foundation.txt", + "data_RNA_Seq_expression_capture.txt", + "data_RNA_Seq_expression_capture_Zscores.txt", + "data_RNA_Seq_expression_capture_all_sample_Zscores.txt", + "data_RNA_Seq_expression_cpm.txt", + "data_RNA_Seq_expression_cpm_Zscores.txt", + "data_RNA_Seq_expression_cpm_all_sample_Zscores.txt", + "data_RNA_Seq_expression_median.txt", + "data_RNA_Seq_expression_tpm.txt", + "data_RNA_Seq_expression_tpm_Zscores.txt", + "data_RNA_Seq_expression_tpm_all_sample_Zscores.txt", + "data_RNA_Seq_mRNA_median_Zscores.txt", + "data_RNA_Seq_mRNA_median_all_sample_Zscores.txt", + "data_RNA_Seq_v2_expression_median.txt", + "data_RNA_Seq_v2_mRNA_median_Zscores.txt", + "data_RNA_Seq_v2_mRNA_median_Zscores_normals.txt", + "data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt", + "data_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt", + "data_RNA_Seq_v2_mRNA_median_normals.txt", + "data_armlevel_CNA.txt", + "data_bcr_clinical_data.txt", + "data_bcr_clinical_data_*.txt", + "data_clinical.txt", + "data_clinical_caises.xml", + "data_clinical_patient.txt", + "data_clinical_sample.txt", + "data_clinical_supp.txt", + "data_clinical_supp_*.txt", + "data_cna_hg18.seg", + "data_cna_hg19.seg", + "data_drug_treatment_AUC.txt", + "data_drug_treatment_IC50.txt", + "data_drug_treatment_ZSCORE.txt", + "data_expression.txt", + "data_expression_Zscores.txt", + "data_expression_all_sample_Zscores.txt", + "data_expression_median.txt", + "data_expression_merged.txt", + "data_expression_merged_Zscores.txt", + "data_expression_merged_median_Zscores.txt", + "data_expression_miRNA.txt", + "data_expression_other_Zscores.txt", + "data_fusions.txt", + "data_fusions_gml.txt", + "data_gene_matrix.txt", + "data_gene_panel.txt", + "data_gene_panel_*.txt", + "data_gistic_genes_amp.txt", + "data_gistic_genes_del.txt", + "data_gsva_pvalues.txt", + "data_gsva_scores.txt", + "data_linear_CNA.txt", + "data_log2CNA.txt", + "data_mRNA_median_Zscores.txt", + "data_mRNA_median_all_sample_Zscores.txt", + "data_mRNA_outliers.txt", + "data_mRNA_seq_fpkm.txt", + "data_mRNA_seq_fpkm_capture.txt", + "data_mRNA_seq_fpkm_capture_Zscores.txt", + "data_mRNA_seq_fpkm_capture_all_sample_Zscores.txt", + "data_mRNA_seq_fpkm_polya.txt", + "data_mRNA_seq_fpkm_polya_Zscores.txt", + "data_mRNA_seq_fpkm_polya_all_sample_Zscores.txt", + "data_methylation_binary.txt", + "data_methylation_genebodies_hmEPIC.txt", + "data_methylation_genebodies_wgbs.txt", + "data_methylation_hm27.txt", + "data_methylation_hm450.txt", + "data_methylation_promoters_hmEPIC.txt", + "data_methylation_promoters_wgbs.txt", + "data_miRNA_median_Zscores.txt", + "data_microbiome.txt", + "data_mrnaseq_fcount.txt", + "data_mrnaseq_rsem.txt", + "data_mutational_signature_contribution_v2.txt", + "data_mutational_signature_contribution_v3.txt", + "data_mutational_signature_pvalue_v2.txt", + "data_mutational_signature_pvalue_v3.txt", + "data_mutations_extended.txt", + "data_mutations_extended_*.txt", + "data_mutations_extended_foundation.txt", + "data_mutations_germline.txt", + "data_mutations_manual.txt", + "data_mutations_nonsignedout.txt", + "data_mutations_uncalled.txt", + "data_mutsig.txt", + "data_phosphoprotein_quantification.txt", + "data_protein_quantification.txt", + "data_protein_quantification_Zscores.txt", + "data_protein_quantification_zscores.txt", + "data_resource_definition.txt", + "data_resource_sample.txt", + "data_resource_study.txt", + "data_rppa.txt", + "data_rppa_Zscores.txt", + "data_timeline.txt", + "data_timeline_*.txt", + "meta_CNA.txt", + "meta_CNA_RAE.txt", + "meta_CNA_consensus.txt", + "meta_CNA_foundation.txt", + "meta_RNA_Seq_expression_capture.txt", + "meta_RNA_Seq_expression_capture_Zscores.txt", + "meta_RNA_Seq_expression_capture_all_sample_Zscores.txt", + "meta_RNA_Seq_expression_cpm.txt", + "meta_RNA_Seq_expression_cpm_Zscores.txt", + "meta_RNA_Seq_expression_cpm_all_sample_Zscores.txt", + "meta_RNA_Seq_expression_median.txt", + "meta_RNA_Seq_expression_tpm.txt", + "meta_RNA_Seq_expression_tpm_Zscores.txt", + "meta_RNA_Seq_expression_tpm_all_sample_Zscores.txt", + "meta_RNA_Seq_mRNA_median_Zscores.txt", + "meta_RNA_Seq_mRNA_median_all_sample_Zscores.txt", + "meta_RNA_Seq_v2_expression_median.txt", + "meta_RNA_Seq_v2_mRNA_median_Zscores.txt", + "meta_RNA_Seq_v2_mRNA_median_Zscores_normals.txt", + "meta_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt", + "meta_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt", + "meta_RNA_Seq_v2_mRNA_median_normals.txt", + "meta_armlevel_CNA.txt", + "meta_bcr_clinical.txt", + "meta_bcr_clinical_other.txt", + "meta_clinical.txt", + "meta_clinical_caises.txt", + "meta_clinical_patient.txt", + "meta_clinical_sample.txt", + "meta_cna_hg18_seg.txt", + "meta_cna_hg19_seg.txt", + "meta_drug_treatment_AUC.txt", + "meta_drug_treatment_IC50.txt", + "meta_drug_treatment_ZSCORE.txt", + "meta_expression.txt", + "meta_expression_Zscores.txt", + "meta_expression_all_sample_Zscores.txt", + "meta_expression_median.txt", + "meta_expression_merged.txt", + "meta_expression_merged_Zscores.txt", + "meta_expression_merged_median_Zscores.txt", + "meta_expression_miRNA.txt", + "meta_expression_other_Zscores.txt", + "meta_fusions.txt", + "meta_fusions_gml.txt", + "meta_gene_matrix.txt", + "meta_gistic_genes_amp.txt", + "meta_gistic_genes_del.txt", + "meta_gsva_pvalues.txt", + "meta_gsva_scores.txt", + "meta_linear_CNA.txt", + "meta_log2CNA.txt", + "meta_mRNA_median_Zscores.txt", + "meta_mRNA_median_all_sample_Zscores.txt", + "meta_mRNA_outliers.txt", + "meta_mRNA_seq_fpkm.txt", + "meta_mRNA_seq_fpkm_capture.txt", + "meta_mRNA_seq_fpkm_capture_Zscores.txt", + "meta_mRNA_seq_fpkm_capture_all_sample_Zscores.txt", + "meta_mRNA_seq_fpkm_polya.txt", + "meta_mRNA_seq_fpkm_polya_Zscores.txt", + "meta_mRNA_seq_fpkm_polya_all_sample_Zscores.txt", + "meta_methylation_binary.txt", + "meta_methylation_genebodies_hmEPIC.txt", + "meta_methylation_genebodies_wgbs.txt", + "meta_methylation_hm27.txt", + "meta_methylation_hm450.txt", + "meta_methylation_promoters_hmEPIC.txt", + "meta_methylation_promoters_wgbs.txt", + "meta_miRNA_median_Zscores.txt", + "meta_microbiome.txt", + "meta_mrnaseq_fcount.txt", + "meta_mrnaseq_rsem.txt", + "meta_mutational_signature_contribution_v2.txt", + "meta_mutational_signature_contribution_v3.txt", + "meta_mutational_signature_pvalue_v2.txt", + "meta_mutational_signature_pvalue_v3.txt", + "meta_mutations_extended.txt", + "meta_mutations_uncalled.txt", + "meta_mutsig.txt", + "meta_phosphoprotein_quantification.txt", + "meta_protein_quantification.txt", + "meta_protein_quantification_Zscores.txt", + "meta_protein_quantification_zscores.txt", + "meta_resource_definition.txt", + "meta_resource_sample.txt", + "meta_resource_study.txt", + "meta_rppa.txt", + "meta_rppa_Zscores.txt", + "meta_timeline.txt" + ] + +def filenames_in_use_before_update(): + """ + this processes the items in FILENAMES_IN_USE_BEFORE_UPDATE_LIST, separating the simple filenames from the wildcard patterns, and returning two results. + """ + filenames_in_use_before_update_set = set() + wildcard_patterns_in_use_before_update_set = set() + for filename in FILENAMES_IN_USE_BEFORE_UPDATE_LIST: + if "*" in filename: + wildcard_patterns_in_use_before_update_set.add(filename) + else: + filenames_in_use_before_update_set.add(filename) + return filenames_in_use_before_update_set, wildcard_patterns_in_use_before_update_set + +def parse_current_datatypes(): + """ + the contents of the datatype sheet (in tab separated format) are parsed and all filenames (both meta and staging) or wildcard patterns are mapped to their associated datatypes. The maps are returned. + + wildcard parterns are returned in a separate dictionary, so that matching can be done using wildcard substitution (rather than exact string match) example: + - data_mutations_uniprot_canonical_transcripts_*.txt is a newly introduced wildcard pattern. In this function, it will be added to the map wildcard_pattern2datatype + wildcard_pattern2datatype['data_mutations_uniprot_canonical_transcripts_*.txt'] = 'mutation-other' + - later, while scanning files, this wildcard pattern will be "split" into two parts (see split_wildcard_patterns()) .. the prefix before the asterisk and the suffix after: + {'prefix' : 'data_mutations_uniprot_canonical_transcripts_', 'suffix' : '.txt'} + - testing for matching files (from the cancer study source directories) will be done using comparisons to these prefix/suffix pairs + """ + datatype_sheet_lines = DATATYPE_SHEET_DOWNLOAD_TAB_SEPARATED.splitlines() + filename2datatype = {} + wildcard_pattern2datatype = {} + header_skipped = False + for line in datatype_sheet_lines: + if not header_skipped: + if line.startswith("datatype"): + header_skipped = True + continue + fields = line.split("\t") + datatype = fields[0].strip() + staging_filename = fields[5].strip() + meta_filename = fields[9].strip() + if "*" in staging_filename: + wildcard_pattern2datatype[staging_filename] = datatype + else: + filename2datatype[staging_filename] = datatype + if "*" in meta_filename: + wildcard_pattern2datatype[meta_filename] = datatype + else: + filename2datatype[meta_filename] = datatype + return filename2datatype, wildcard_pattern2datatype + +def is_normal_sample_filename(filename): + """ + examines filename to see if the importer would skip it as a "normal sample" file. + """ + normal_sample_suffixes = ["_normals.txt", "data_mrna_seq_v2_rsem_normal_samples.txt", "data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt"] + for suffix in normal_sample_suffixes: + if filename.endswith(suffix): + return True; + return False; + +def split_wildcard_patterns(wildcard_patterns): + """ + breaks a list of wildcard_patterns (each containing a single asterisk) into two parts, returning a list of dictionaries with prefix/suffix. + """ + split_wildcard_pattern_list = [] + for wildcard_pattern in wildcard_patterns: + pattern_segments = wildcard_pattern.strip().split("*") + if len(pattern_segments) != 2: + sys.stderr.write("Error : wildcard filename pattern '" + wildcard_pattern + "' does not have exactly one asterisk\n") + sys.exit(1) + split_wildcard_pattern = {"prefix" : pattern_segments[0], "suffix" : pattern_segments[1]} + split_wildcard_pattern_list.append(split_wildcard_pattern) + return split_wildcard_pattern_list + +def matches_wildcard_pattern(filename, split_wildcard_pattern): + """ + returns True if filename starts with the prefix from, and ends with the suffix from, the split_wildcard_pattern dictionary. + + example : when split_wildcard_pattern is {'prefix' : 'data_mutations_uniprot_canonical_transcripts_', 'suffix' : '.txt'} this function will return: + - True for a file such as "data_mutations_uniprot_canonical_transcripts_uniprot.txt", and + - False for a file such as "meta_mutations_uniprot_canonical_transcripts_uniprot.txt" + """ + return filename.startswith(split_wildcard_pattern["prefix"]) and filename.endswith(split_wildcard_pattern["suffix"]) + +def matches_any_wildcard_pattern(filename, split_wildcard_patterns): + """ + iterates through all pattern dictionaries, looking for any match for filename. + """ + for split_wildcard_pattern in split_wildcard_patterns: + if matches_wildcard_pattern(filename, split_wildcard_pattern): + return True + return False + +def study_directory_uses_original_filenames(path): + """ + determines if unsupported filename patterns (those added June 2021) are present or not in a study directory + + search directory at - return False if any unsupported filenames are present, which: + - are not of the original set of filenames we recognized before the renaming effort, and + - would be imported according to the current datatypes sheet, and + - are not "normal sample" files (which are ignored by the importer) + + arguments: + path -- the (absolute or relative) filename path to the directory which should be examined + """ + new_filenames_present = False + if os.path.isdir(path): + path = path + os.path.sep + basedir = os.path.dirname(path) + filenames = os.listdir(path) + original_datatype_filenames, original_wildcard_patterns = filenames_in_use_before_update() + current_datatype_filenames, current_wildcard_patterns = parse_current_datatypes() + split_original_wildcard_patterns = split_wildcard_patterns(original_wildcard_patterns) + split_current_wildcard_patterns = split_wildcard_patterns(current_wildcard_patterns) + for filename in filenames: + filepath = os.path.join(basedir, filename) + if not os.path.isfile(filepath): + # ignore subdirectories + continue + if filename in original_datatype_filenames or matches_any_wildcard_pattern(filename, split_original_wildcard_patterns): + # ignore original filenames and matches to any original wildcard pattern + continue + if not filename in current_datatype_filenames and not matches_any_wildcard_pattern(filename, split_current_wildcard_patterns): + # filename/pattern was not found in current list - so would be skipped by importer + continue + if is_normal_sample_filename(filename): + # normal sample files are skipped in importer + continue + print("file '%s' is an updated filename for the datatype" % filename) + new_filenames_present = True + return not new_filenames_present + +def main(args): + """ + scans a study directory for any novel filenames which are not yet supported by the merge scripts + returns non-zero if novel/updated/unsupported filenames are preset, 0 otherwise + """ + if study_directory_uses_original_filenames(args.cancer_study_path): + sys.exit(0); + else: + sys.exit(1); + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description = 'scans a study directory for any novel filenames which are not yet supported by the merge scripts - exits with non-0 if any are found') + parser.add_argument("-d", "--directory_of_study", action="store", required=True, dest="cancer_study_path") + args = parser.parse_args() + main(args) diff --git a/import-scripts/subset-impact-data.sh b/import-scripts/subset-impact-data.sh index 09ce19c36..3087d63c0 100755 --- a/import-scripts/subset-impact-data.sh +++ b/import-scripts/subset-impact-data.sh @@ -55,6 +55,14 @@ if [ -z $PORTAL_SCRIPTS_DIRECTORY ]; then fi echo -e "\tPORTAL_SCRIPTS_DIRECTORY="$PORTAL_SCRIPTS_DIRECTORY +# check for presence of new filename pattens (not yet supported) and fail if present + +$PYTHON_BINARY $PORTAL_SCRIPTS_DIRECTORY/study_directory_uses_original_filenames.py -d $INPUT_DIRECTORY +if [ $? -ne 0 ] ; then + echo "unsupported filenames present - skipping subset" >&2 + exit 1 +fi + # status flags GEN_SUBSET_LIST_FAILURE=0 MERGE_SCRIPT_FAILURE=0 @@ -106,7 +114,7 @@ if [ $STUDY_ID == "genie" ]; then $PYTHON_BINARY $PORTAL_SCRIPTS_DIRECTORY/add-age-at-seq-report.py --clinical-file="$OUTPUT_DIRECTORY/data_clinical_supp_sample.txt" --seq-date-file="$INPUT_DIRECTORY/cvr/seq_date.txt" --age-file="$INPUT_DIRECTORY/ddp/ddp_age.txt" --convert-to-days="true" if [ $? -gt 0 ] ; then echo "Failed to add AGE_AT_SEQ_REPORT to $OUTPUT_DIRECTORY/data_clinical_supp_sample.txt using $INPUT_DIRECTORY/cvr/seq_date.txt. Exiting..." - exit 2l + exit 2 fi # rename GENE_PANEL to SEQ_ASSAY_ID in data_clinical_supp_sample.txt diff --git a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_patient.txt b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_patient.txt index e69de29bb..9b725af71 100644 --- a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_patient.txt +++ b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_patient.txt @@ -0,0 +1 @@ +cancer_study_identifier: crdb_pdx_raw_data diff --git a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_sample.txt b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_sample.txt index e69de29bb..9b725af71 100644 --- a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_sample.txt +++ b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_clinical_sample.txt @@ -0,0 +1 @@ +cancer_study_identifier: crdb_pdx_raw_data diff --git a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_timeline.txt b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_timeline.txt index e69de29bb..9b725af71 100644 --- a/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_timeline.txt +++ b/import-scripts/test/resources/subset_and_merge_pdx/data_repos/crdb_pdx_repos/crdb_pdx_raw_data/meta_timeline.txt @@ -0,0 +1 @@ +cancer_study_identifier: crdb_pdx_raw_data