From 5014f649e37a5e704a834f3b427c8041267adb23 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Wed, 4 Dec 2013 21:29:59 -0500
Subject: [PATCH] Added unit tests for sampleFile program.
---
test/sample/human.hg19.genome | 94 +++++++++++++++++++++++
test/sample/sample-intersect.sh | 124 +++++++++++++++++++++++++++++++
test/sample/sample-intersect.sh~ | 124 +++++++++++++++++++++++++++++++
test/sample/sample_help.txt | 34 +++++++++
test/sample/test-sample.sh | 124 +++++++++++++++++++++++++++++++
test/test.sh | 6 +-
6 files changed, 505 insertions(+), 1 deletion(-)
create mode 100644 test/sample/human.hg19.genome
create mode 100644 test/sample/sample-intersect.sh
create mode 100644 test/sample/sample-intersect.sh~
create mode 100644 test/sample/sample_help.txt
create mode 100644 test/sample/test-sample.sh
diff --git a/test/sample/human.hg19.genome b/test/sample/human.hg19.genome
new file mode 100644
index 00000000..d22ce2d6
--- /dev/null
+++ b/test/sample/human.hg19.genome
@@ -0,0 +1,94 @@
+
+chr1 249250621
+chr10 135534747
+chr11 135006516
+chr11_gl000202_random 40103
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr17_ctg5_hap1 1680828
+chr17_gl000203_random 37498
+chr17_gl000204_random 81310
+chr17_gl000205_random 174588
+chr17_gl000206_random 41001
+chr18 78077248
+chr18_gl000207_random 4262
+chr19 59128983
+chr19_gl000208_random 92689
+chr19_gl000209_random 159169
+chr1_gl000191_random 106433
+chr1_gl000192_random 547496
+chr2 243199373
+chr20 63025520
+chr21 48129895
+chr21_gl000210_random 27682
+chr22 51304566
+chr3 198022430
+chr4 191154276
+chr4_ctg9_hap1 590426
+chr4_gl000193_random 189789
+chr4_gl000194_random 191469
+chr5 180915260
+chr6 171115067
+chr6_apd_hap1 4622290
+chr6_cox_hap2 4795371
+chr6_dbb_hap3 4610396
+chr6_mann_hap4 4683263
+chr6_mcf_hap5 4833398
+chr6_qbl_hap6 4611984
+chr6_ssto_hap7 4928567
+chr7 159138663
+chr7_gl000195_random 182896
+chr8 146364022
+chr8_gl000196_random 38914
+chr8_gl000197_random 37175
+chr9 141213431
+chr9_gl000198_random 90085
+chr9_gl000199_random 169874
+chr9_gl000200_random 187035
+chr9_gl000201_random 36148
+chrM 16571
+chrUn_gl000211 166566
+chrUn_gl000212 186858
+chrUn_gl000213 164239
+chrUn_gl000214 137718
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chrUn_gl000218 161147
+chrUn_gl000219 179198
+chrUn_gl000220 161802
+chrUn_gl000221 155397
+chrUn_gl000222 186861
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000225 211173
+chrUn_gl000226 15008
+chrUn_gl000227 128374
+chrUn_gl000228 129120
+chrUn_gl000229 19913
+chrUn_gl000230 43691
+chrUn_gl000231 27386
+chrUn_gl000232 40652
+chrUn_gl000233 45941
+chrUn_gl000234 40531
+chrUn_gl000235 34474
+chrUn_gl000236 41934
+chrUn_gl000237 45867
+chrUn_gl000238 39939
+chrUn_gl000239 33824
+chrUn_gl000240 41933
+chrUn_gl000241 42152
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000244 39929
+chrUn_gl000245 36651
+chrUn_gl000246 38154
+chrUn_gl000247 36422
+chrUn_gl000248 39786
+chrUn_gl000249 38502
+chrX 155270560
+chrY 59373566
diff --git a/test/sample/sample-intersect.sh b/test/sample/sample-intersect.sh
new file mode 100644
index 00000000..f7f5f11d
--- /dev/null
+++ b/test/sample/sample-intersect.sh
@@ -0,0 +1,124 @@
+###########################################################
+#
+# Unit tests for sampleFile program
+#
+############################################################
+
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+#
+# Create a 1,000 record BED6 file named "mainFile.bed".
+# Give it a one line header, to test the -header option.
+#
+###########################################################
+echo "#This is the mainFile from which samples will be taken." > mainFile.bed
+$BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
+
+
+
+###########################################################
+# Test that help is printed when no args are given
+############################################################
+echo " sample.t01...\c"
+$BT sample 2>&1 > /dev/null | cat - > obs
+check obs sample_help.txt
+rm obs
+
+
+###########################################################
+# Test that we throw an error for unrecognized arguments
+############################################################
+echo " sample.new.t02...\c"
+echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp
+$BT sample -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when no input file is given
+############################################################
+echo " sample.new.t03...\c"
+echo "***** ERROR: input file not specified. *****" > exp
+$BT sample -n 10 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -i without input file
+############################################################
+echo " sample.new.t04...\c"
+echo "***** ERROR: -i option given, but no input file specified. *****" > exp
+$BT sample -i 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -n given without
+# number of output records sepcified.
+############################################################
+echo " sample.new.t05...\c"
+echo "***** ERROR: -n option given, but no number of output records specified. *****" > exp
+$BT sample -n 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when num output records
+# exceeds records in file.
+############################################################
+echo " sample.new.t06...\c"
+echo "***** ERROR: Input file has fewer records than the requested number of output records. *****" > exp
+$BT sample -i mainFile.bed 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we get the requested number of records
+############################################################
+echo " sample.new.t07...\c"
+echo 10 > exp
+$BT sample -i mainFile.bed -n 10 | wc -l | cut -f1 --delimiter=' '> obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that the -seed option gives consistent results
+############################################################
+echo " sample.new.t08...\c"
+$BT sample -i mainFile.bed -n 50 -seed 4 > obs
+$BT sample -i mainFile.bed -n 50 -seed 4 > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that -header option gives header
+############################################################
+echo " sample.new.t09...\c"
+echo "#This is the mainFile from which samples will be taken." > exp
+$BT sample -i mainFile.bed -n 10 -header | head -1 > obs
+check obs exp
+rm obs exp
+
+rm mainFile.bed
+
+
+
+
+
diff --git a/test/sample/sample-intersect.sh~ b/test/sample/sample-intersect.sh~
new file mode 100644
index 00000000..9356193f
--- /dev/null
+++ b/test/sample/sample-intersect.sh~
@@ -0,0 +1,124 @@
+###########################################################
+#
+# Unit tests for sampleFile program
+#
+############################################################
+
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+#
+# Create a 1,000 record BED6 file named "mainFile.bed".
+# Give it a one line header, to test the -header option.
+#
+###########################################################
+echo "#This is the mainFile from which samples will be taken." > mainFile.bed
+$BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
+
+
+
+###########################################################
+# Test that help is printed when no args are given
+############################################################
+echo " sample.t01...\c"
+$BT sample 2>&1 > /dev/null | cat - > obs
+check obs sample_help.txt
+rm obs
+
+
+###########################################################
+# Test that we throw an error for unrecognized arguments
+############################################################
+echo " sample.new.t02...\c"
+echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp
+$BT sample -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when no input file is given
+############################################################
+echo " sample.new.t03...\c"
+echo "***** ERROR: input file not specified. *****" > exp
+$BT sample -n 10 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -i without input file
+############################################################
+echo " sample.new.t04...\c"
+echo "***** ERROR: -i option given, but no input file specified. *****" > exp
+$BT sample -i 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -n given without
+# number of output records sepcified.
+############################################################
+echo " sample.new.t05...\c"
+echo "***** ERROR: -n option given, but no number of output records specified. *****" > exp
+$BT sample -n 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when num output records
+# exceeds records in file.
+############################################################
+echo " sample.new.t06...\c"
+echo "***** ERROR: Input file has fewer records than the requested number of output records. *****" > exp
+$BT sample -i mainFile.bed 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we get the requested number of records
+############################################################
+echo " sample.new.t07...\c"
+echo 10 > exp
+$BT sample -i mainFile.bed -n 10 | wc -l | cut -f1 --delimiter=' '> obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that the -seed option gives consistent results
+############################################################
+echo " sample.new.t08...\c"
+$BT sample -i mainFile.bed -n 50 -seed 4 > obs
+$BT sample -i mainFile.bed -n 50 -seed 4 > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that -header option gives header
+############################################################
+echo " sample.new.t09...\c"
+echo "#This is the mainFile from which samples will be taken." > exp
+$BT sample -i mainFile.bed -n 10 -header | head -1 > exp
+check obs exp
+rm obs exp
+
+rm mainFile.bed
+
+
+
+
+
diff --git a/test/sample/sample_help.txt b/test/sample/sample_help.txt
new file mode 100644
index 00000000..b291966a
--- /dev/null
+++ b/test/sample/sample_help.txt
@@ -0,0 +1,34 @@
+
+Tool: bedtools sample (aka sampleFile)
+Version: v2.17.0-144-gb1aa9ab-dirty
+Summary: Take sample of input file(s) using reservoir sampling algorithm.
+
+Usage: bedtools sample [OPTIONS] -i <bed/gff/vcf/bam>
+
+WARNING: The current sample algorithm will hold all requested sample records in memory prior to output.
+ The user must ensure that there is adequate memory for this.
+
+Options:
+ -n The number of records to generate.
+ - Default = 1,000,000.
+ - (INTEGER)
+
+ -seed Supply an integer seed for the shuffling.
+ - By default, the seed is chosen automatically.
+ - (INTEGER)
+
+ -ubam Write uncompressed BAM output. Default writes compressed BAM.
+
+ -bed When using BAM input (-abam), write output as BED. The default
+ is to write output in BAM when using -abam.
+
+ -s Require same strandedness. That is, only give records
+ that have the same strand. Use '-s forward' or '-s reverse'
+ for forward or reverse strand records, respectively.
+ - By default, records are reported without respect to strand.
+
+ -header Print the header from the input file prior to results.
+
+Notes:
+ TBD: Enter other usage notes here.
+
diff --git a/test/sample/test-sample.sh b/test/sample/test-sample.sh
new file mode 100644
index 00000000..f7f5f11d
--- /dev/null
+++ b/test/sample/test-sample.sh
@@ -0,0 +1,124 @@
+###########################################################
+#
+# Unit tests for sampleFile program
+#
+############################################################
+
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+#
+# Create a 1,000 record BED6 file named "mainFile.bed".
+# Give it a one line header, to test the -header option.
+#
+###########################################################
+echo "#This is the mainFile from which samples will be taken." > mainFile.bed
+$BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
+
+
+
+###########################################################
+# Test that help is printed when no args are given
+############################################################
+echo " sample.t01...\c"
+$BT sample 2>&1 > /dev/null | cat - > obs
+check obs sample_help.txt
+rm obs
+
+
+###########################################################
+# Test that we throw an error for unrecognized arguments
+############################################################
+echo " sample.new.t02...\c"
+echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp
+$BT sample -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when no input file is given
+############################################################
+echo " sample.new.t03...\c"
+echo "***** ERROR: input file not specified. *****" > exp
+$BT sample -n 10 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -i without input file
+############################################################
+echo " sample.new.t04...\c"
+echo "***** ERROR: -i option given, but no input file specified. *****" > exp
+$BT sample -i 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -n given without
+# number of output records sepcified.
+############################################################
+echo " sample.new.t05...\c"
+echo "***** ERROR: -n option given, but no number of output records specified. *****" > exp
+$BT sample -n 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when num output records
+# exceeds records in file.
+############################################################
+echo " sample.new.t06...\c"
+echo "***** ERROR: Input file has fewer records than the requested number of output records. *****" > exp
+$BT sample -i mainFile.bed 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we get the requested number of records
+############################################################
+echo " sample.new.t07...\c"
+echo 10 > exp
+$BT sample -i mainFile.bed -n 10 | wc -l | cut -f1 --delimiter=' '> obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that the -seed option gives consistent results
+############################################################
+echo " sample.new.t08...\c"
+$BT sample -i mainFile.bed -n 50 -seed 4 > obs
+$BT sample -i mainFile.bed -n 50 -seed 4 > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that -header option gives header
+############################################################
+echo " sample.new.t09...\c"
+echo "#This is the mainFile from which samples will be taken." > exp
+$BT sample -i mainFile.bed -n 10 -header | head -1 > obs
+check obs exp
+rm obs exp
+
+rm mainFile.bed
+
+
+
+
+
diff --git a/test/test.sh b/test/test.sh
index f624846b..7eafcc55 100644
--- a/test/test.sh
+++ b/test/test.sh
@@ -29,7 +29,7 @@ echo " Testing bedtools getfasta:"
cd getfasta; sh test-getfasta.sh; cd ..
echo " Testing bedtools intersect:"
-cd intersect; sh test-intersect.sh; sh new_test-intersect.sh cd ..
+cd intersect; sh test-intersect.sh; sh new_test-intersect.sh; cd ..
echo " Testing bedtools jaccard:"
cd jaccard; sh test-jaccard.sh; cd ..
@@ -51,3 +51,7 @@ cd slop; sh test-slop.sh; cd ..
echo " Testing bedtools subtract:"
cd subtract; sh test-subtract.sh; cd ..
+
+echo " Testing bedtools sample:"
+cd sample; sh test-sample.sh; cd ..
+
--
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