def test_hisat2():
#test hisat build and hisat mapping
hs=mapping.Hisat2(index=os.path.join(testVars.testDir,"hisatindex"),genome=testVars.genome)
assert hs.check_index()==True, "Failed hisat buildindex"
#perform alignment without sraobject
kwargs={"-1":testVars.fq1,"-2":testVars.fq2,"-S":testVars.testDir+"/hisatTest.sam","--dta-cufflinks":"","-p":"4"}
st=hs.run(**kwargs)
assert st==True, "Failed to run hisat"
def test_hisat2():
#test hisat build and hisat mapping
hsOpts = {"--dta-cufflinks": "", "-p": "10"}
hs = mapping.Hisat2(hisat2_index="", **hsOpts)
assert hs.check_index() == False, "Failed hisat check_index"
#build index
st = hs.build_index(testVars.testDir, "hisatindex", testVars.genome)
assert st == True, "Failed to build hisat2 index"
#perform alignment without sraobject
hsMapOpts = {
"-1": testVars.fq1,
"-2": testVars.fq2,
"-S": testVars.testDir + "/hisatTest.sam"
}
st = hs.run_hisat2(**hsMapOpts)
assert st == True, "Failed to run hisat"
def test_pipeline1():
sraOb = sra.SRA(srr, workingDir)
st = sraOb.download_sra()
assert st == True, "SRA download failed"
st = sraOb.run_fasterqdump(delete_sra=False,
**{
"-e": "8",
"-f": "",
"-t": workingDir
})
assert st == True, "fqdump failed"
bbdOpts = {
"ktrim": "r",
"k": "23",
"mink": "11",
"qtrim": "'rl'",
"trimq": "10",
"--": ("-Xmx2g", ),
"ref": testVars.bbdukAdapters
}
bbdOb = qc.BBmap(**bbdOpts)
st = sraOb.perform_qc(bbdOb)
assert st == True, "bbduk failed"
tgOpts = {
"--cores": "10",
"-o": testVars.testDir,
"--paired": "",
"--": (fq1, fq2)
}
tg = qc.Trimgalore(**tgOpts)
st = sraOb.perform_qc(tg)
assert st == True, "tg failed"
#runbowtie2
bt = mapping.Bowtie2(bowtie2_index="")
assert bt.check_index() == False, "Failed bowtie2 check_index"
st = bt.build_index(testVars.testDir + "/btIndex", "bowtieIndex",
testVars.genome)
assert st == True, "Failed to build bowtie2 index"
st = bt.perform_alignment(sraOb)
assert os.path.isfile(st) == True, "bowtie failed"
hsOpts = {"--dta-cufflinks": "", "-p": "8"}
hs = mapping.Hisat2(hisat2_index="", **hsOpts)
st = hs.build_index(testVars.testDir, "hisatindex", testVars.genome)
assert st == True, "Failed to build hisat2 index"
#perform alignment with sraobject
st = hs.perform_alignment(sraOb)
assert os.path.isfile(st) == True, "hisat failed"
hisatSam = st
samOb = tools.Samtools(**{"-@": "8"})
bam = samOb.sam_sorted_bam(hisatSam, delete_sam=False, delete_bam=False)
assert os.path.isfile(bam) == True, "sam to bam failed"
stie = assembly.Stringtie(reference_gtf=testVars.gtf)
result = stie.perform_assembly(bam, out_dir=testVars.testDir)
assert pu.check_files_exist(result) == True, "Failed stringtie"
tr = assembly.Trinity()
tr_out = tr.perform_assembly(sraOb, verbose=True)
assert pu.check_files_exist(tr_out) == True, "Failed stringtie"
kl = quant.Kallisto(kallisto_index="")
assert kl.check_index() == False, "Failed kallisto check_index"
st = kl.build_index(index_path=testVars.testDir + "/kallistoIndex",
index_name="kalIndex",
fasta=testVars.cdna)
assert st == True, "Failed to build kallisto index"
st = kl.perform_quant(sraOb)
assert os.path.isdir(st) == True, "Failed to run kallisto"
sl = quant.Salmon(salmon_index="")
assert sl.check_index() == False, "Failed salmon check_index"
st = sl.build_index(index_path=testVars.testDir + "/salmonIndex",
index_name="salIndex",
fasta=testVars.cdna)
assert st == True, "Failed to build salmon index"
st = sl.perform_quant(sraOb)
assert os.path.isdir(st) == True, "Failed to run salmon"
bbdOb = qc.BBmap(**bbdOpts)
for ob in sraObjects:
ob.perform_qc(bbdOb)
for ob in sraObjects:
print("SRR Accession: {}, fastq files: {}. {}".format(
ob.srr_accession, ob.localfastq1Path, ob.localfastq2Path))
if ob.fastqFilesExistsLocally():
print("Both files exist!!")
else:
print("Error")
raise Exception("Fastq files not found")
hsOpts = {"--dta-cufflinks": "", "-p": "16"}
hs = mapping.Hisat2(hisat2_index="", **hsOpts)
hisat2_buildArgs = {"-p": "16", "-a": "", "-q": ""}
if hs.build_index(workingDir + "/maizeIndex", "maizeInd", GENOME,
**hisat2_buildArgs):
print("Indexing done.")
if hs.check_index():
print("Index {} exists".format(hs.hisat2_index))
samList = []
for ob in sraObjects:
print("Processing {}...".format(ob.srr_accession))
thisSam = hs.perform_alignment(ob, **{"-p": "16"})
if thisSam:
samList.append(thisSam)
#create objects
bbdOpts = {
"ktrim": "r",
"k": "23",
"mink": "11",
"qtrim": "'rl'",
"trimq": "10",
"ref": testVars.bbdukAdapters
}
bbdOb = qc.BBmap(None, **bbdOpts)
tg = qc.Trimgalore()
bt = mapping.Bowtie2(index=testVars.testDir + "/btIndex",
genome=testVars.genome)
hsOpts = {"--dta-cufflinks": "", "-p": "8"}
hs = mapping.Hisat2(index=testVars.testDir + "/hisatindex",
genome=testVars.genome,
**hsOpts)
star = mapping.Star(index=os.path.join(testVars.testDir, "starIndex"),
genome=testVars.genome)
samOb = tools.Samtools()
stie = assembly.Stringtie()
kl = quant.Kallisto(index=testVars.testDir + "/kallistoIndex/kalIndex",
transcriptome=testVars.cdna)
sl = quant.Salmon(index=testVars.testDir + "/salmonIndex/salIndex",
transcriptome=testVars.cdna_big)
#sra ob
sraOb = sra.SRA(srr, workingDir)
st = sraOb.fastq_exists()
assert st == True, "fasterq-dump failed"
#run bbmap
#bd=qc.BBmap()
#sraOb.performQC(bd)
#run bowtie
#bob=mapping.Bowtie2(btIndex)
#unMappedReads=bob.runBowTie2(sraOb)
#update fastq as
#sraOb.localfastqPath=unMappedReads
#build hisat index
hsOpts={"--dta-cufflinks":"","-p":"12","--mp": "1,1", "--no-spliced-alignment":"", "--rdg": "10000,10000", "--rfg": "10000,10000"}
hs=mapping.Hisat2(hisat2_index="/home/usingh/work/urmi/hoap/test/yeastInd2/index22",**hsOpts)
#hsbArgs={"-p":"8","-a":"","-q":""}
#if hs.buildHisat2Index("/home/usingh/work/urmi/hoap/test/yeastInd2","index22","/home/usingh/work/urmi/hoap/test/hisatYeast/S288C_reference_genome_R64-2-1_20150113/S288C_reference_sequence_R64-2-1_20150113.fsa",**hsbArgs):
# print("Success")
#run hisat
sam=hs.perform_alignment(sraOb,**{"--dta-cufflinks":"","-p":"8"})
#get sorted bam
samOb=tools.Samtools(**{"-@":"8"})
bam=samOb.sam_sorted_bam(sam,delete_sam=True,delete_bam=True)
#bt2=mapping.Bowtie2("/home/usingh/work/urmi/hoap/test/bowtieIndex/rRNAindex")
#bt2.performAlignment(sraOb)