def getReads(readsDir):
readsExt = workerForBam.getExtDict()["READS_EXT"]
dirContents = os.listdir(readsDir)
reads = []
for name in dirContents:
if os.path.isfile(os.path.join(readsDir, name)) and name.endswith(readsExt):
reads.append(name)
return reads
def writeJob(jobsFile, fastaFilePath, lockDirPath, tools):
extensions = workerForBam.getExtDict()
#fasta file name
fastaFileName = (fastaFilePath.split('/')[-1]).split('.')[0]
#fasta dir
fastaDir = '/'.join(fastaFilePath.split('/')[:-1]) + '/'
#job lock file path for current job
currentJobLockFile = lockDirPath + "SNPS" + fastaFileName
#check for lock file in case current job is already executed
jobsFile.write("if [ -f " + currentJobLockFile \
+ ".lock ]; then echo \"" \
+ currentJobLockFile \
+" done\"; exit 0; ")
#check if job is already finished
jobsFile.write("elif [ -f " + currentJobLockFile \
+ ".out ]; then echo \"" \
+ currentJobLockFile \
+" done\"; exit 0; ")
jobsFile.write("else ")
#need to execute job
#write lock file b4 executing job
jobsFile.write("touch "+currentJobLockFile+".lock; ")
#write statements for processing job
#change directory to scaffold where we are working
jobsFile.write("cd "+ fastaDir+"; ")
#generate fai
jobsFile.write(tools['SAMTOOLS'] + " faidx "\
+ fastaDir + fastaFileName + extensions['SCAFF_EXT'] +\
" ; ")
#built fasta sequence dictionary
jobsFile.write("java -Xms2048m -jar " + tools['PICARD_TOOLS']\
+ "/CreateSequenceDictionary.jar R=" + fastaFilePath\
+ " O=" + fastaDir + fastaFileName +".dict ; ")
#merge all bams for this scaffold into single bama
jobsFile.write(tools['SAMTOOLS'] + " merge "\
+ fastaDir + fastaFileName + extensions['UNIQ_SORT_BAM_EXT'] + ".bam "\
+ fastaDir + "*" + extensions['UNIQ_SORT_BAM_EXT'] + ".bam "\
+ " ; ")
#add or replace read groups
jobsFile.write("java -Xms2048m -jar " + tools['PICARD_TOOLS']\
+ "/AddOrReplaceReadGroups.jar I="\
+ fastaDir + fastaFileName\
+ extensions['UNIQ_SORT_BAM_EXT'] + ".bam O="\
+ fastaDir + fastaFileName + "_picard2.sorted.bam"\
+ " SORT_ORDER=coordinate RGLB=1 RGPL=illumina RGPU=bar" \
+ " RGSM=BMGC VALIDATION_STRINGENCY=LENIENT"\
+ " CREATE_INDEX=TRUE ; ")
#reorder SAM
jobsFile.write("java -Xms2048m -jar " + tools['PICARD_TOOLS']\
+ "/ReorderSam.jar I="\
+ fastaDir + fastaFileName + "_picard2.sorted.bam"\
+ " O="+fastaDir + fastaFileName\
+ "_picard3.sorted.bam " + "REFERENCE="+fastaFilePath\
+ " VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE ; ")
#genome analysis tK realigner target creator
jobsFile.write("java -Xms2048m -jar " + tools['GENOME_ANALYSIS_TK_JAR']\
+ " -T RealignerTargetCreator -R " + fastaFilePath\
+ " -I " + fastaDir + fastaFileName\
+ "_picard3.sorted.bam -o " + fastaDir + fastaFileName\
+ ".intervals ; ")
#genome analysis tK indel realigner
jobsFile.write("java -Xms2048m -jar " + tools['GENOME_ANALYSIS_TK_JAR']\
+ " -T IndelRealigner -R " + fastaFilePath\
+ " -I " + fastaDir + fastaFileName\
+ "_picard3.sorted.bam -targetIntervals "\
+ fastaDir + fastaFileName\
+ ".intervals -o " + fastaDir + fastaFileName\
+ "_gatkrealigned.sorted.bam ; ")
#sangerq sorted bam
#TODO: where is sangerq used
"""jobsFile.write(tools['SAMTOOLS'] + " view -h " + fastaDir + fastaFileName\
+ "_gatkrealigned.sorted.bam | perl -lane '$\"=\"\\t\";"\
+ " if (/^@/) {print;} else {$F[10]=~ tr/\\x40-\\xff"\
+ "\\x00-\\x3f/\\x21-\\xe0\\x21/;print \"@F\"}' | )"\
+ tools['SAMTOOLS'] + " view -Sbh - > " + fastaDir\
+ fastaFileName + "_gatkrealigned_sangerQ.sorted.bam; ")"""
#mpileup generation
jobsFile.write(tools['SAMTOOLS'] + " mpileup -BQ0 -d10000000 -f "\
+ fastaFilePath + " " + fastaDir + fastaFileName\
+ "_gatkrealigned.sorted.bam > " + fastaDir\
+ fastaFileName +"_gatkrealigned.mpileup ; ")
#use varscan to make realigned cns
jobsFile.write("java -jar " + tools['VARSCAN_JAR'] +" mpileup2cns "\
+ fastaDir + fastaFileName +"_gatkrealigned.mpileup"\
+ " --min-coverage 8 --min-reads2 3 --min-avg-qual 20"\
+ " --min-var-freq 0.01 --p-value 0.99 --strand-filter"\
+ " 0 --variants 1 > " + fastaDir + fastaFileName\
+ "_realigned.cns ; ")
#generate indels
jobsFile.write("java -jar " + tools['VARSCAN_JAR'] + " mpileup2indel "\
+ fastaDir + fastaFileName + "_gatkrealigned.mpileup"\
+ " --min-coverage 8 --min-reads2 3 --min-avg-qual 20"\
+ " --min-var-freq 0.01 --p-value 0.99 --strand-filter 0"\
+ " --variants 1 > " + fastaDir + fastaFileName\
+ "_realigned2.indel ; ")
#rename mpileup to pileup
jobsFile.write("mv " + fastaDir + fastaFileName + "_gatkrealigned.mpileup "\
+ fastaDir + fastaFileName + "_gatkrealigned.pileup ; ")
#pileup to SNP
jobsFile.write("java -jar " + tools['VARSCAN_JAR'] + " pileup2snp "\
+ fastaDir + fastaFileName + "_gatkrealigned.pileup"\
+ " --min-coverage 8 --min-reads2 3 --min-avg-qual 20"\
+ " --min-var-freq 0.01 --p-value 0.99 > "\
+ fastaDir + fastaFileName + "_realigned3.snp ")
#create lock.out file indicating completion
jobsFile.write("; touch " + currentJobLockFile + ".out ")
jobsFile.write("; fi")
jobsFile.write("\n")
