diff test-data/create_test-data @ 0:6e75a84e9338 draft

planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/create_test-data	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,104 @@
+#!/bin/bash
+source ~/env/bin/activate
+
+samtools faidx chrMT.fa
+#TEST1: single read, with everything default
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1
+mv out_read1.fq chrMT_read1.fq
+
+#TEST2: PE reads, with everything default
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30
+mv out_read1.fq chrMT-PE_read1.fq
+mv out_read2.fq chrMT-PE_read2.fq
+
+#TEST3: PE reads, with everything default, now with VCF and BAM files
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam
+mv out_read1.fq chrMT-PE-VCF-BAM_read1.fq
+mv out_read2.fq chrMT-PE-VCF-BAM_read2.fq
+mv out_golden.bam chrMT-PE-VCF-BAM.bam
+mv out_golden.vcf chrMT-PE-VCF-BAM.vcf
+
+samtools index chrMT-PE-VCF-BAM.bam
+
+#TEST4: PE reads, with VCF and BAM files and VCF file from TEST3 as the seed
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam -v chrMT-PE-VCF-BAM.vcf
+mv out_read1.fq chrMT-PE-VCF-BAM-vcf_read1.fq
+mv out_read2.fq chrMT-PE-VCF-BAM-vcf_read2.fq
+mv out_golden.bam chrMT-PE-VCF-BAM-vcf.bam
+mv out_golden.vcf chrMT-PE-VCF-BAM-vcf.vcf
+
+samtools index chrMT-PE-VCF-BAM-vcf.bam
+
+#TEST5: PE reads, with VCF and BAM files and BED file as the targeted region
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam -t chrMT-Targets.bed -to 0.02
+mv out_read1.fq chrMT-PE-VCF-BAM-Targeted_read1.fq
+mv out_read2.fq chrMT-PE-VCF-BAM-Targeted_read2.fq
+mv out_golden.bam chrMT-PE-VCF-BAM-Targeted.bam
+mv out_golden.vcf chrMT-PE-VCF-BAM-Targeted.vcf
+
+samtools index chrMT-PE-VCF-BAM-Targeted.bam
+
+#TEST6: PE reads, with everything default, now with VCF and BAM files GZIPPED
+python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam --gz
+mv out_read1.fq.gz chrMT-PE-VCF-BAM-gz_read1.fq.gz
+mv out_read2.fq.gz chrMT-PE-VCF-BAM-gz_read2.fq.gz
+mv out_golden.bam chrMT-PE-VCF-BAM-gz.bam
+#Galaxy does not support gzipped VCF file (not sure if this is BGZIPPED)
+gunzip out_golden.vcf.gz && mv out_golden.vcf chrMT-PE-VCF-BAM-gz.vcf
+
+samtools index chrMT-PE-VCF-BAM-gz.bam
+
+#TEST7: PE reads, with all error parameters changed, with VCF and BAM files, not compressed 
+python2 ../genReads.py -r chrMT.fa -R 151 -o out --rng 123 --pe 500 50 --vcf --bam -c 20 -E 0.123 -M 0.123 -p 3
+mv out_read1.fq chrMT-PE-VCF-BAM-panic_read1.fq
+mv out_read2.fq chrMT-PE-VCF-BAM-panic_read2.fq
+mv out_golden.bam chrMT-PE-VCF-BAM-panic.bam
+mv out_golden.vcf chrMT-PE-VCF-BAM-panic.vcf
+
+samtools index chrMT-PE-VCF-BAM-panic.bam
+
+#####
+# computeGC TESTS
+#
+
+#TEST1: Use BAM from TEST3 to create the model file. Window size = 10
+bedtools genomecov -d -ibam chrMT-PE-VCF-BAM.bam -g chrMT.fa > chrMT-PE-VCF-BAM.genomecov
+python2 ../utilities/computeGC.py -r chrMT.fa -i chrMT-PE-VCF-BAM.genomecov -w 10 -o chrMT-PE-VCF-BAM-computeGC.p
+
+#####
+# computeFraglen
+#
+samtools view chrMT-PE-VCF-BAM.bam | python2 ../utilities/computeFraglen.py
+mv fraglen.p chrMT-PE-VCF-BAM-fraglen.p
+
+#####
+# genMutModel
+#
+
+#TEST1: Default settings
+python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-genMutModel.p
+
+#TEST2: Defined include list
+python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-INCLUDELIST-genMutModel.p\
+        -bi chrMT-Targets.bed
+
+#TEST3: Defined exclude list
+python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-EXCLUDELIST-genMutModel.p\
+        -be chrMT-Targets.bed
+		
+#TEST1: Default settings with all booleans set to YES
+python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-BOOLEANS-genMutModel.p\
+        --save-trinuc --no-whitelist --skip-common
+
+#####
+# genSeqErrorModel
+#
+
+#TEST1 - 100,000 simulations - Single read
+python2 ../utilities/genSeqErrorModel.py -i chrMT_read1.fq -s 100000 -o chrMT_read1_genSeqErrorModel.p
+
+#TEST2 - 100,000 simulations - Paired reads
+python2 ../utilities/genSeqErrorModel.py -i chrMT-PE_read1.fq -i2 chrMT-PE_read2.fq -s 100000 -o chrMT-PE_read1_genSeqErrorModel.p
+
+#TEST3 - 100,000 simulations - Only 100 reads
+python2 ../utilities/genSeqErrorModel.py -i chrMT-PE_read1.fq -i2 chrMT-PE_read2.fq -s 100000 -o chrMT-PE-100reads_read1_genSeqErrorModel.p -n 100