Document data sources

test/BigBed-test.js

@@ -10,10 +10,7 @@ var ContigInterval = require('../src/ContigInterval');
 
 describe('BigBed', function() {
   function getTestBigBed() {
-    // This file was generated using UCSC tools:
-    // cd kent/src/utils/bedToBigBed/tests; make
-    // It is compressed, little endian, has autoSQL and two blocks.
-    return new BigBed('/test/data/itemRgb.bb');
+    return new BigBed('/test/data/itemRgb.bb');   // See test/data/README.md
   }
 
   it('should extract features in a range', function(done) {

test/BigBedDataSource-test.js

@@ -10,11 +10,7 @@ var BigBed = require('../src/BigBed'),
 
 describe('BigBedDataSource', function() {
   function getTestSource() {
-    // This file was created from Biodalliance's ensGene.bb via:
-    // bigBedToBed ensGene.bb ensGene.bed
-    // grep '^chr17\t' ensGene.bed > /tmp/ensGene17.bed
-    // bedToBigBed -type=bed12+2 /tmp/ensGene17.bed <(echo "chr17 78774742")
-    //             test/data/ensembl.chr17.bb
+    // See test/data/README.md
     return createBigBedDataSource(new BigBed('/test/data/ensembl.chr17.bb'));
   }
 

test/TwoBit-test.js

@@ -9,11 +9,7 @@ var TwoBit = require('../src/TwoBit');
 
 describe('TwoBit', function() {
   function getTestTwoBit() {
-    // This file was generated using UCSC tools:
-    // twoBitToFa -seqList=./test/seqList.txt hg19.2bit /tmp/extract.fa
-    // perl -i -pe 's/:.*//' /tmp/extract.fa
-    // faToTwoBit /tmp/extract.fa test/data/test.2bit
-    return new TwoBit('/test/data/test.2bit');
+    return new TwoBit('/test/data/test.2bit');   // See test/data/README.md
   }
 
   it('should have the right contigs', function(done) {

test/components-test.js

@@ -45,7 +45,7 @@ describe('Root component', function() {
   var dataSource = createTwoBitDataSource(genome);
 
   // This file contains just the TP53 gene, shifted so that it starts at the
-  // beginning of chr17 (to match test.2bit).
+  // beginning of chr17 (to match test.2bit). See test/data/README.md.
   var ensembl = new BigBed('/test/data/tp53.shifted.bb');
   var ensemblDataSource = createBigBedDataSource(ensembl);
 

test/data/README.md

@@ -0,0 +1,49 @@
+This directory contains many small data files used in testing.
+
+This file documents how they were generated.
+
+
+#### test.2bit
+
+This is a small subset of the hg19 reference genome. It contains small swaths
+of chr1 and chr22 and a larger swath of chr17. It was generated from hg19.2bit
+using UCSC tools:
+
+    curl -O http://www.biodalliance.org/datasets/hg19.2bit
+    twoBitToFa -seqList=./test/data/seqList.txt hg19.2bit /tmp/extract.fa
+    perl -i -pe 's/:.*//' /tmp/extract.fa
+    faToTwoBit /tmp/extract.fa test/data/test.2bit
+
+
+#### itemRgb.bb, itemRgb.bed
+
+This file was generated from UCSC test data:
+
+    cd kent/src/utils/bedToBigBed/tests
+    make
+    cp output/itemRgb.bb $PILEUP/test/data/
+
+It is compressed, little endian, has autoSQL and two blocks.
+
+`itemRgb.bed` is copied unmodified from `bedToBigBed/tests/input`.
+
+
+#### ensembl.chr17.bb
+
+This file is derived from `ensGene.bb`. It contains just the genes on chr17.
+
+    curl -O http://www.biodalliance.org/datasets/ensGene.bb
+    bigBedToBed ensGene.bb ensGene.bed
+    grep '^chr17\t' ensGene.bed > /tmp/ensGene17.bed
+    bedToBigBed -type=bed12+2 /tmp/ensGene17.bed <(echo "chr17 78774742") test/data/ensembl.chr17.bb
+
+#### tp53.shifted.bb
+
+This is a subset of `ensembl.chr17.bb`, shifted to match the coordinates in
+`test.2bit`:
+
+    curl -O http://www.biodalliance.org/datasets/ensGene.bb
+    bigBedToBed ensGene.bb ensGene.bed
+    grep '^chr17\t' ensGene.bed | grep TP53 | perl -pe 's/(75\d{4,})/$1-7512444/ge' > /tmp/tp53.shifted.bed
+    bedToBigBed -type=bed12+2 /tmp/tp53.shifted.bed <(echo "chr17 78774742") test/data/tp53.shifted.bb
+