Add test files with 'chr' prefix added to seqnames (#177)

* add test files with 'chr' prefix added to seqnames * note about chr_prefix files in tests/test_data/README.md
iRNA-COSI · Sep 28, 2021 · 4a204b3 · 4a204b3
1 parent ca33f6a
commit 4a204b3
Show file tree

Hide file tree

Showing 9 changed files with 1,114 additions and 1 deletion.
diff --git a/tests/test_data/README.md b/tests/test_data/README.md
@@ -2,8 +2,9 @@
 Use the files provided here for developing, debugging, testing your code.
 
 * `.bam` files with index files (`.bam.bai`) as inputs for execution workflows ([Created by choosing 2 genes with MACE-seq PAS reads at at least 2 sites (GSE151724) and subsetting bam files (generated for the pilot_benchmark: siControl_R1, SRR11918577 and siSrsf3_R1, SRR11918579) to reads contain reads falling within +/- 1kb from gene boundaries from the gtf file]).
-* `.fastq` files can be generated to test alignments using `samtools bam2fq input.bam > output.fastq`. 
+* `.fastq` files can be generated to test alignments using `samtools bam2fq input.bam > output.fastq`.
 * corresponding `.gtf` ([Created GENCODE release M18 subsetted to the 2 genes for the test data with leading "chr" removed to match bam files])
 * corresponding `.gff3` ([Created GENCODE release M18 subsetted to the 2 genes for the test data with leading "chr" removed to match bam files])
 * `.MACEseq.mm10.bed` as a ground truth example files ([BED6 files for clevage and poly(A) sites for the 2 genes from the two samples (siControl_R1, SRR11918617 and siSrsf3_R2, SRR11918619) where the score column corresponds to the TPM for each PAS detected by MACE-seq in that sample])
+* `.bam`, `.bam.bai`, `.gtf`, `.gff3` and `.bed` files containing `_Chr_prefix` in the filename. These were generated from their counterparts without the string by adding a `chr` prefix has been added to the fields with chromosome names.
 * [EXTEND THIS LIST WHEN ADDING MORE TEST FILES TO THE DIRECTORY]
diff --git a/tests/test_data/gencode_2genes_Chr_prefix.vM18.annotation.gff3 b/tests/test_data/gencode_2genes_Chr_prefix.vM18.annotation.gff3
diff --git a/tests/test_data/gencode_2genes_Chr_prefix.vM18.annotation.gtf b/tests/test_data/gencode_2genes_Chr_prefix.vM18.annotation.gtf
diff --git a/tests/test_data/siControl_R1_2genes_Chr_prefix.MACEseq.mm10.bed b/tests/test_data/siControl_R1_2genes_Chr_prefix.MACEseq.mm10.bed
@@ -0,0 +1,6 @@
+chr6	119923969	119923970	dPAS_9821	174.961985532	-
+chr6	119925550	119925551	pPAS_9822	25.4490160774	-
+chr16	78336750	78336751	pPAS_1596	12.7245080387	+
+chr16	78340181	78340182	oPAS_1597	12.7245080387	+
+chr16	78340750	78340751	oPAS_1598	162.237477494	+
+chr16	78359782	78359783	dPAS_1599	6.36225401935	+
diff --git a/tests/test_data/siControl_R1_2genes_Chr_prefix.bam b/tests/test_data/siControl_R1_2genes_Chr_prefix.bam
diff --git a/tests/test_data/siControl_R1_2genes_Chr_prefix.bam.bai b/tests/test_data/siControl_R1_2genes_Chr_prefix.bam.bai
diff --git a/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.MACEseq.mm10.bed b/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.MACEseq.mm10.bed
@@ -0,0 +1,6 @@
+chr6	119923969	119923970	dPAS_9821	180.804499064	-
+chr6	119925550	119925551	pPAS_9822	72.861514548	-
+chr16	78336750	78336751	pPAS_1596	32.3828953547	+
+chr16	78340181	78340182	oPAS_1597	8.09572383867	+
+chr16	78340750	78340751	oPAS_1598	83.6558129996	+
+chr16	78359782	78359783	dPAS_1599	13.4928730644	+
diff --git a/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.bam b/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.bam
diff --git a/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.bam.bai b/tests/test_data/siSrsf3_R1_2genes_Chr_prefix.bam.bai