def test_stringtie():
bam = testVars.hisatSortedBam
gtf = testVars.gtf
stie = assembly.Stringtie(reference_gtf=gtf)
result = stie.perform_assembly(bam,
out_dir=testVars.testDir,
objectid="test")
assert pu.check_files_exist(result) == True, "Failed stringtie"
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"
samOb = tools.Samtools(**{"-@": "16"})
bamList = []
i = 0
for sam in samList:
print("Processing:" + sam)
thisBam = samOb.sam_sorted_bam(sam,
delete_sam=True,
delete_bam=True,
objectid=sraObjects[i].srr_accession)
i += 1
if thisBam:
bamList.append(thisBam)
print("Sorted bam files:" + ",".join(bamList))
st = assembly.Stringtie()
gtfList = []
i = 0
for bam in bamList:
print("Processing:" + bam)
gtfList.append(
st.perform_assembly(bam,
objectid=sraObjects[i].srr_accession,
**{
"-m": "150",
"-p": "16"
}))
i += 1
print("Final GTFs:" + ",".join(gtfList))
"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"
def test_pipeline1():
st = sraOb.trim(bbdOb).align(hs).assemble(stie).quant(kl)
assert st != None, "pipeline 1 failed"
idsfile = sys.argv[1]
analysis = sys.argv[2]
runquant = False
runalign = False
if analysis == 'quant': runquant = True
if analysis == 'align': runalign = True
with open(idsfile) as f:
data = f.read().splitlines()
#set infile dir as workdir
basedir = pu.get_file_directory(idsfile)
#pyrpipe objects
star = mapping.Star()
#Create stringtie object
stieobj = assembly.Stringtie()
#biobambam
biobb = Bamtofastq()
#salmon for quant
salmon = quant.Salmon()
#delete final sorted bam
delete_bam = True
#out_dir is same name as input file
out_dir = basedir
progresslog = open(idsfile + '_progress.log', 'w')
bam_suffix = '.Aligned.sortedByCoord.out.patched.md.bam'
#process each bam
for line in data:
temp = line.split('\t')
#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)
#run stringtie
st=assembly.Stringtie()
g1=st.perform_assembly(bam,objectid="myob")
#gtfs=(g1,)
#test stmerge
#merged=st.performStringtieMerge(g1,g1,outFileSuffix="_stOUT",overwrite=True)
#if not merged:
# print("Fail")
"""
bamList=[]
sraObList=[]
for s in ['SRR5507495','SRR5507442','SRR5507362']:
sraOb=sra.SRA(s,testDir)
#download sra
sraOb.downloadSRAFile()