####################################################################################################
# Starting pipeline at Tue Sep 26 17:20:53 EEST 2017
# Input files:  test.fastq
# Output Log:  .bpipe/logs/34518.log
# Stage preprocess
cat test.fastq | ../scripts/fastqToFASTA.pl 2> test.fastq.processing |cutadapt -a TCGTATGCCGTCTTCTGCTTG -g AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC -b CGTACGCGGGTTTAAACGA -b CGTACGCGGAATAGTTTAAACTGT -n 1 -m 20 - 2>> test.fastq.processing | ../scripts/collapseFA.pl > test.fasta
# Stage align
bowtie ../files/hg19 -v 1 -m 10 --best --strata -p 4 -S --un unaligned_test.fasta -f test.fasta --quiet | samtools view -hS -F 4 - > test.aligned.sam
# Stage PARparams
perl ../scripts/editPARalyzerINIfile.pl ../scripts/Default_PARalyzer_Parameters.ini test.aligned.sam ../files/GRCh37.p12.genome.2bit > test.ini
# Stage PARalyze
../scripts/PARalyzer 8G test.ini
mv test_PARalyzer_Utilized.sam test.sam
# Stage sam2bam
samtools view -bhS test.sam  | samtools sort -o - - > test.bam
# Stage index
samtools index test.bam
# Stage readAttributes
../scripts/readAttributesTC.pl test.sam > test.attr
# Stage annotateReads
../scripts/annotate.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -p ../scripts/annotationRank.txt -r ../files/hg19_rmsk.bed.gz -s ../files/hg19_rmsk_info -strict -oi test.attr > test.readcsv
# Stage read_bed
../scripts/reads2bed.py test.readcsv > test.readbed
# Stage annotateClusters
../scripts/annotate.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -p ../scripts/annotationRank.txt -r ../files/hg19_rmsk.bed.gz -s ../files/hg19_rmsk_info -strict -oi test.clusters | ../scripts/PARclusters2bed.py > test.clusterbed
# Stage addInfo
intersectBed -a test.readbed -b test.clusterbed -wao -s | 		awk -F "	" 'BEGIN{OFS=",";} { print  		$5,$7,$8,$9,$11,$12}' | sed '/,\-1/d' | 		../scripts/editClustersTC.pl .6 > test.clusters.csv
# Stage visbed
cat test.clusters.csv | ../scripts/visclusterbed.py > test.clusters.bed
# Stage geneLvl
perl ../scripts/geneLevel.pl test.clusters.csv ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz > test.gene_cl.csv
# ########## Finished at Tue Sep 26 17:25:47 EEST 2017 Duration = 4 minutes, 54.123 seconds ##########


####################################################################################################
# Starting pipeline at Tue Sep 26 18:00:49 EEST 2017
# Input files:  test.fastq
# Output Log:  .bpipe/logs/60197.log
# Stage preprocess
# Stage align
# Stage PARparams
# Stage PARalyze
# Stage sam2bam
# Stage index
# Stage readAttributes
# Stage annotateReads
# Stage read_bed
# Stage annotateClusters
# Stage addInfo
# Stage visbed
# Stage geneLvl
# Stage annotateGroups
../scripts/annotate.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -p ../scripts/annotationRank.txt -r ../files/hg19_rmsk.bed.gz -s ../files/hg19_rmsk_info -strict -oi test.groups | ../scripts/PARclusters2bed.py > test.groupbed
# Stage addInfoGroups
intersectBed -a test.readbed -b test.groupbed -wao -s | 		awk -F "	" 'BEGIN{OFS=",";} { print  		$5,$7,$8,$9,$11,$12}' | sed '/,\-1/d' | 		../scripts/editClustersTC.pl > test.groups.csv
# Stage geneLvlGroups
perl ../scripts/geneLevel.pl test.groups.csv ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz > test.gene_gr.csv
# Stage statsTable
../scripts/extractDataTC.pl test > test.clusters.txt
# Stage spatialPerl
perl ../scripts/Spatial.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -a test -strict -t ../files/isoforms.fpkm_tracking
# Stage spatialR
unset TMP; unset TEMP; TEMPDIR="/tmp/47608273698326195-0"  setsid  Rscript - <<'!'
            
		yn<-'n'
		fn<-'test'
		resolution<-3
		install.packages('../scripts/colorRamps_2.3.tar.gz', lib='../scripts/')
		install.packages('../scripts/schoolmath_0.4.tar.gz', lib='../scripts/')
		install.packages('../scripts/gtools_3.4.1.tar.gz', lib='../scripts/')
		install.packages('../scripts/ellipse_0.3-8.tar.gz', lib='../scripts/')
		install.packages('../scripts/RColorBrewer_1.1-2.tar.gz', lib='../scripts/')
		install.packages('../scripts/LSD_2.5.tar.gz', lib='../scripts/')
		library(colorRamps, lib.loc='../scripts/')
		library(schoolmath, lib.loc='../scripts/')
		library(gtools, lib.loc='../scripts/')
		library(ellipse, lib.loc='../scripts/')
		library(RColorBrewer, lib.loc='../scripts/')
		library(LSD, lib.loc='../scripts/')
		library(parallel)
		source('../scripts/Spatial.R')
	
!

# ########## Finished at Tue Sep 26 18:02:28 EEST 2017 Duration = 1 minutes, 39.191 seconds ##########