def test_salmon():
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"
opts = {
"-o": testVars.testDir + "/salOut",
"-l": "A",
"-1": testVars.fq1,
"-2": testVars.fq2
}
st = sl.run_salmon("quant", **opts)
assert st == True, "Failed to run salmon"
def test_salmon():
sl=quant.Salmon(index=testVars.testDir+"/salmonIndex/salIndex",transcriptome=testVars.cdna_big)
assert sl.check_index()==True, "Failed salmon build_index"
opts={"-o":testVars.testDir+"/salOut",
"-l":"A",
"-1":testVars.fq1,
"-2":testVars.fq2}
st=sl.run(subcommand='quant',target='tests/testout/salOut/quant.sf',**opts)
assert st==True, "Failed to run salmon"
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(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"
def test_pipeline2():
st = sraOb.trim(tg).align(hs).assemble(stie).quant(kl)
assert st != None, "pipeline 2 failed"
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')
sampleid = temp[0]
#add fid to out dir
this_outdir = os.path.join(basedir, sampleid)
pu.mkdir(this_outdir)