Bug fix: bad sequences included in ASM pattern result

Take filtered sequences as ASM input. Update demo description and test data correspondingly.

BSPAT_standAlone/README.md

@@ -14,14 +14,15 @@ Reference: [Hu, K., Ting, A. H., & Li, J. (2015). BSPAT: a fast online tool for
 
 # 2.Prerequisite
 * Java 1.8 or higher
-* Bismark and its required softwares
+* Bismark and its required softwares (e.g. python, samtools, bowtie2)
 
 ##2.1 install
 Unzip BSPAT_standALone zip file. Executable files are under bin folder.
 
 To add BSPAT to $PATH, [check here](http://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable)
 
 # 3.Demo
+Following demo is tested with bowtie2-2.3.4.2-linux-x86_64, Bismark_v0.19.1, samtools1.6
 [Download demo data](demo.zip)
 
 Demo folder structure:
@@ -69,28 +70,28 @@ After execution, demo folder looks like:
 
 ## 3.2 BSPAT
 ```
->BSPAT ref demoSequence.fastq_bismark.bam target.bed
+>BSPAT ref demoSequence_bismark_bt2.bam target.bed
 ```
 Result files are:
 ```
 .
-├── demo-31-99-test_bismark.analysis_ASM.txt
-├── demo-31-99-test_bismark.analysis_Methylation.txt
-├── demo-31-99-test_bismark.analysis_MethylationWithSNP.txt
-├── demo-31-99-test_bismark.analysis_report.txt
-├── demo-31-99-test_bismark.analysis.txt
+├── demo-31-99-test-plus_bismark.analysis_ASM.txt
+├── demo-31-99-test-plus_bismark.analysis_Methylation.txt
+├── demo-31-99-test-plus_bismark.analysis_MethylationWithSNP.txt
+├── demo-31-99-test-plus_bismark.analysis_report.txt
+├── demo-31-99-test-plus_bismark.analysis.txt
 
 ```
 ## 3.3 BSPAT_figure
 ```
->BSPAT_figure demo-31-99-test_bismark.analysis_Methylation.txt demo-31-99-test_bismark.analysis_report.txt
->BSPAT_figure demo-31-99-test_bismark.analysis_ASM.txt -a
+>BSPAT_figure demo-31-99-test-plus_bismark.analysis_Methylation.txt demo-31-99-test-plus_bismark.analysis_report.txt
+>BSPAT_figure demo-31-99-test-plus_bismark.analysis_ASM.txt -a
 ```
 Result files are:
 ```
 .
-├── demo-31-99-test_bismark.analysis_ASM.png
-├── demo-31-99-test_bismark.analysis_Methylation.png
+├── demo-31-99-test_bismark-plus.analysis_ASM.png
+├── demo-31-99-test_bismark-plus.analysis_Methylation.png
 ```
 
 # 4.Interface

BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/CLI/BSPAT_pgm.java

@@ -171,7 +171,13 @@ private static void generatePatternsSingleGroup(String outputPath, double bisulf
 		Pair<List<Sequence>, List<Sequence>> qualityFilterSequencePair = filterSequences(
 				seqGroup, bisulfiteConversionRate, sequenceIdentityThreshold);
 
+		List<Sequence> sequenceNotPassedQualityFilter = qualityFilterSequencePair.getRight();
+		System.out.printf("%d unqualified sequences are filtered.\n", sequenceNotPassedQualityFilter.size());
+		IOUtils.writeAnalysedSequences(outputPath + "/" + targetRegion.toString() + "_bismark.analysis.filtered.txt",
+				sequenceNotPassedQualityFilter, refSeq.length(), targetRegion.isMinusStrand());
+
 		List<Sequence> sequencePassedQualityFilter = qualityFilterSequencePair.getLeft();
+		System.out.printf("%d qualified sequences are included in result.\n", sequencePassedQualityFilter.size());
 		IOUtils.writeAnalysedSequences(outputPath + "/" + targetRegion.toString() + "_bismark.analysis.txt",
 				sequencePassedQualityFilter, refSeq.length(), targetRegion.isMinusStrand());
 
@@ -212,7 +218,7 @@ private static void generatePatternsSingleGroup(String outputPath, double bisulf
 					Pattern.METHYLATIONWITHSNP),
 					targetRefSeq, meMuPatternList, Pattern.METHYLATIONWITHSNP, sequencePassedQualityFilter.size());
 
-			Pair<Pattern, Pattern> allelePatterns = getAllelePatterns(seqGroup, potentialSNP);
+			Pair<Pattern, Pattern> allelePatterns = getAllelePatterns(sequencePassedQualityFilter, potentialSNP);
 			Pattern allelePattern = allelePatterns.getLeft();
 			Pattern nonAllelePattern = allelePatterns.getRight();
 			if (allelePattern.getCount() != 0 && nonAllelePattern.getCount() != 0) {

BSPAT_standAlone/src/test/resources/integration/demoExpected/demoRef-10-96-test-plus_bismark.analysis_ASM.txt

@@ -1,14 +1,14 @@
 ASM	count	percentage
 TCTCTAATGAGGGAGGAGGCCCGAGGATGGCTGGGTTTGATTTATGACTGGAGGAGAAGGTCCACTTCCCACTGCGAAGCAGGCGAC	ref
----------------------**---------------------------------------------------**-------**--	417	0.5291878172588832
----------------------@@---------------------------------------------------@@-------@A--	371	0.47081218274111675
+---------------------**---------------------------------------------------**-------**--	410	0.5203045685279187
+---------------------@@---------------------------------------------------@@-------@A--	356	0.4517766497461929
 Methylation level in reads with reference allele:
 Relative_CpG_position	Methyl_Level
-21	0.08173076923076923
-74	0.9206730769230769
-83	0.7718446601941747
+21	0.08068459657701711
+74	0.921760391198044
+83	0.7728395061728395
 Methylation level in reads with alternative allele:
 Relative_CpG_position	Methyl_Level
-21	0.0972972972972973
-74	0.16172506738544473
-83	0.02981029810298103
+21	0.09859154929577464
+74	0.1601123595505618
+83	0.022598870056497175