TCGA_BreastCancer_FilteredSomaticMutations_RNAExpression
Status: Complete
Testing Directory . . .
Results: PASS
Testing Configuration File . . .
✅ config.yaml contains all necessary configurations.
✅ Title is less than 100 characters
✅ description.md contains a description.
Results: PASS
Running Install . . .
Executing install.sh: Success
Results: PASS
Testing file paths:
✅ test_data.tsv exists.
✅ test_metadata.tsv exists.
✅ download.sh exists.
✅ install.sh exists.
✅ parse.sh exists.
✅ cleanup.sh exists.
✅ description.md exists.
✅ config.yaml exists.
Running user code . . .
Executing download.sh: Success
Executing parse.sh: Success
✅ data.tsv.gz was created and zipped correctly.
✅ metadata.tsv.gz was created and zipped correctly.
Results: PASS
Testing Key Files:
✅ test_data.tsv contains enough unique samples to test
✅ test_data.tsv contains enough test cases (8; min: 8)
✅ test_metadata.tsv contains enough unique samples to test
✅ test_metadata.tsv contains enough test cases (16; min: 8)
Results: PASS
First 5 columns and 5 rows of data.tsv.gz:
| Sample | 1/2-SBSRNA4 | A1BG | A1BG-AS1 | A1CF |
|---|---|---|---|---|
| TCGA-3C-AAAU-01A-11R-A41B-07 | 5.54232446204596 | 12.9679516712473 | 3.14176915832577 | 0.00520202913308217 |
| TCGA-3C-AALI-01A-11R-A41B-07 | 3.39482819338405 | 17.1577035101616 | 4.32682026222599 | 0.118286519300192 |
| TCGA-3C-AALJ-01A-31R-A41B-07 | 2.50640106626595 | 31.6096061992498 | 2.866475585645 | 0.102975760042304 |
| TCGA-3C-AALK-01A-11R-A41B-07 | 1.84821794433028 | 13.2984130137491 | 1.61465988642 | 0.02062411320675 |
Columns: 23369 Rows: 944
“data.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
Results: PASS
First 3 columns and 5 rows of metadata.tsv.gz:
| Sample | Variable | Value |
|---|---|---|
| TCGA-3C-AAAU-01A-11R-A41B-07 | form_completion_date | 2014-1-13 |
| TCGA-3C-AAAU-01A-11R-A41B-07 | prospective_collection | NO |
| TCGA-3C-AAAU-01A-11R-A41B-07 | retrospective_collection | YES |
| TCGA-3C-AAAU-01A-11R-A41B-07 | gender | FEMALE |
Columns: 3 Rows: 118957
“metadata.tsv.gz” Test Cases (from rows in test file). . .
✅ First column of file is titled “Sample”
⚠ The value for variable "days_to_initial_pathologic_diagnosis" for all samples is the same ("0"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "informed_consent_verified" for all samples is the same ("YES"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "tumor_tissue_site" for all samples is the same ("Breast"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "clinical_T" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "disease_code" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "project_code" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_er_positivity_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_pr_positivity_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_pr_positivity_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_positivity_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_positivity_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_signal_number" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_cent_17_signal_number" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "her2_cent17_counted_cells_count" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_cent17_her2_other_scale" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
⚠ The value for variable "nte_her2_fish_define_method" for all samples is the same ("[Not Available]"). This variable has been removed from metadata.tsv.gz
✅ Row 1: Success
✅ Row 2: Success
✅ Row 3: Success
✅ Row 4: Success
✅ Row 5: Success
✅ Row 6: Success
✅ Row 7: Success
✅ Row 8: Success
✅ Row 9: Success
✅ Row 10: Success
✅ Row 11: Success
✅ Row 12: Success
✅ Row 13: Success
✅ Row 14: Success
✅ Row 15: Success
✅ Row 16: Success
Results: PASS
Comparing samples in both files . . .
✅ Samples are the same in both “data.tsv.gz” & “metadata.tsv.gz”