ENCD-5531 adding h5ad file format (#3566)

ENCODE-DCC · Oct 7, 2020 · e3a99e5 · e3a99e5
1 parent 8f044d0
commit e3a99e5
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Showing 5 changed files with 9 additions and 5 deletions.
diff --git a/src/encoded/schemas/changelogs/file.md b/src/encoded/schemas/changelogs/file.md
@@ -2,10 +2,12 @@
 
 ### Schema version 25
 * *output_type* *smoothed methylation stage at CpG* was updated to *smoothed methylation state at CpG*
+* *file_format* was updated to include *h5ad*.
 
 ### Minor changes since schema version 24
 * The *output_type* enum was updated to include *UV enriched segment quantifications*, *plus strand methylation state at CpG*, *minus strand methylation state at CpG*, *CpG sites coverage*, and *sparse gene count matrix*.
 
+
 ### Schema version 24
 * *output_type: stable peaks* was updated to *output_type: pseudo-replicated peaks*
 

diff --git a/src/encoded/schemas/file.json b/src/encoded/schemas/file.json
@@ -839,6 +839,7 @@
                                         "gff",
                                         "gtf",
                                         "idx",
+                                        "h5ad",
                                         "hdf5",
                                         "hic",
                                         "PWM",
@@ -1052,6 +1053,7 @@
                         "fastq",
                         "gff",
                         "gtf",
+                        "h5ad",
                         "hdf5",
                         "hic",
                         "idat",
@@ -2112,6 +2114,7 @@
         "gtf": ".gtf.gz",
         "idx": ".idx",
         "hic": ".hic",
+        "h5ad": ".h5ad",
         "hdf5": ".h5",
         "idat": ".idat",
         "PWM":".pwm",

diff --git a/src/encoded/tests/data/inserts/expected_batch_download.tsv b/src/encoded/tests/data/inserts/expected_batch_download.tsv
@@ -112,4 +112,4 @@ http://localhost/files/ENCFF129DNA/@@download/ENCFF129DNA.bigWig
 http://localhost/files/ENCFF127ACM/@@download/ENCFF127ACM.fastq.gz
 http://localhost/files/ENCFF718LJW/@@download/ENCFF718LJW.bam
 http://localhost/files/ENCFF081AVF/@@download/ENCFF081AVF.bed.gz
-http://localhost/files/ENCFF001SCR/@@download/ENCFF001SCR.bigWig
+http://localhost/files/ENCFF001SCR/@@download/ENCFF001SCR.h5ad
diff --git a/src/encoded/tests/data/inserts/expected_metadata.tsv b/src/encoded/tests/data/inserts/expected_metadata.tsv
@@ -112,4 +112,4 @@ ENCFF129DNA	bigWig	bigWig		signal of all reads	hg19	ENCSR751YPU	DNase-seq	UBERON
 ENCFF127ACM	fastq	fastq		reads		ENCSR604DNT	DNase-seq	UBERON:0001891	midbrain	tissue	Homo sapiens											DNA						2020-01-04	Roadmap				1	1_1	50		single-ended					13689	John Stamatoyannopoulos, UW	d49c217e369df785177805b864542e88		http://localhost/files/ENCFF127ACM/@@download/ENCFF127ACM.fastq.gz		Illumina HiSeq 2000		released			missing documents	
 ENCFF718LJW	bam	bam		alignments	GRCh38	ENCSR604DNT	DNase-seq	UBERON:0001891	midbrain	tissue	Homo sapiens											DNA						2020-01-04	Roadmap				1	1_1							/files/ENCFF127ACM/	145214	John Stamatoyannopoulos, UW	eabe445821ad629815edc9875994f256		http://localhost/files/ENCFF718LJW/@@download/ENCFF718LJW.bam				released		missing analysis_step_run	missing documents	
 ENCFF081AVF	bed narrowPeak	bed	narrowPeak	footprints	GRCh38	ENCSR604DNT	DNase-seq	UBERON:0001891	midbrain	tissue	Homo sapiens											DNA						2020-01-04	Roadmap				1	1_1							/files/ENCFF718LJW/	18390	John Stamatoyannopoulos, UW	d53c4aee0153037136cab8c35d2bb6ca		http://localhost/files/ENCFF081AVF/@@download/ENCFF081AVF.bed.gz				released		missing analysis_step_run	missing documents	
-ENCFF001SCR	bigWig	bigWig		sparse gene count matrix	GRCh38	ENCSR000SCR	scRNA-seq	EFO:0002067	K562	cell line																			ENCODE													370148294	Barbara Wold, Caltech	128ecf542a35ac5270a87dc740918404		http://localhost/files/ENCFF001SCR/@@download/ENCFF001SCR.bigWig	V19			in progress		missing analysis_step_run	missing documents	
+ENCFF001SCR	h5ad	h5ad		sparse gene count matrix	GRCh38	ENCSR000SCR	scRNA-seq	EFO:0002067	K562	cell line																			ENCODE													370148294	Barbara Wold, Caltech	128ecf542a35ac5270a87dc740918404		http://localhost/files/ENCFF001SCR/@@download/ENCFF001SCR.h5ad	V19			in progress		missing analysis_step_run	missing documents	
diff --git a/src/encoded/tests/data/inserts/file.json b/src/encoded/tests/data/inserts/file.json
@@ -4096,7 +4096,7 @@
         "submitted_by": "facilisi.tristique@potenti.vivamus",
         "md5sum": "128ecf542a35ac5270a87dc740918404",
         "accession": "ENCFF001SCR",
-        "file_format": "bigWig",
+        "file_format": "h5ad",
         "award": "/awards/U54HG006998/",
         "assembly": "GRCh38",
         "genome_annotation": "V19",
@@ -4106,8 +4106,7 @@
         "file_size": 370148294,
         "output_type": "sparse gene count matrix",
         "lab": "/labs/barbara-wold/",
-        "aliases": [],
-        "notes": "File format not yet supported for this output_type (expecting h5ad)"
+        "aliases": ["encode:hdf5-sparse-count-matrix"]
     },
     {
         "status": "released",