def assembleWithStringTie(infiles, outfile):
infile, reference = infiles
job_threads = PARAMS["stringtie_threads"]
job_memory = PARAMS["stringtie_memory"]
statement = '''stringtie %(infile)s
-p %(stringtie_threads)s
-G <(zcat %(reference)s)
%(stringtie_options)s
2> %(outfile)s.log
| gzip > %(outfile)s '''
if infile.endswith(".remote"):
token = glob.glob("gdc-user-token*")
tmpfilename = P.getTempFilename()
if len(token) > 0:
token = token[0]
else:
token = None
s, infile = Sra.process_remote_BAM(
infile,
token,
tmpfilename,
filter_bed=os.path.join(
PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs_bed"]))
infile = " ".join(infile)
statement = "; checkpoint ;".join(
["mkdir %(tmpfilename)s", s, statement, "rm -r %(tmpfilename)s"])
P.run()
def quantifyWithSalmon(infiles, outfile):
'''Quantify existing samples against genesets'''
job_threads = 2
job_memory = "16G"
infile, gtffile = infiles
basefile = os.path.basename(infile)
sample_name = basefile.split(os.extsep, 1)
sorted_bam = "sorted_bams/" + sample_name[0] + "_sorted.bam"
gtfbase = P.snip(os.path.basename(gtffile), ".gz")
salmonIndex = "salmon_index/" + gtfbase + ".salmon.index"
fastq1 = P.snip(outfile, "_agg-agg-agg") + ".1.fastq"
fastq2 = P.snip(outfile, "_agg-agg-agg") + ".2.fastq"
salmon_options = PARAMS["salmon_quantoptions"]
statement = '''
samtools sort -n %(infile)s -o %(sorted_bam)s;
samtools fastq
-1 %(fastq1)s
-2 %(fastq2)s
-0 /dev/null -s /dev/null -n -F 0x900
%(sorted_bam)s;
salmon quant -i %(salmonIndex)s
--libType IU
-1 %(fastq1)s
-2 %(fastq2)s
-o %(outfile)s
%(salmon_options)s;
mv %(outfile)s/quant.sf %(outfile)s.sf;
rm %(fastq1)s; rm %(fastq2)s; rm %(sorted_bam)s
'''
if infile.endswith(".remote"):
token = glob.glob("gdc-user-token*")
filename = "temp_bams/%s" % basefile
tmpfilename = P.get_temp_filename()
if os.path.exists(tmpfilename):
os.unlink(tmpfilename)
if len(token) > 0:
token = token[0]
else:
token = None
s, infile = Sra.process_remote_BAM(
infile,
token,
filename,
filter_bed=os.path.join(
PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs_bed"]))
infile = " ".join(infile)
statement = "; ".join(
["mkdir %(filename)s", s, statement, "rm -r %(filename)s"])
P.run(statement)
def downloadFiles(infiles, outfile):
infile = infiles
basefile = os.path.basename(infile)
filename = "temp_bams/%s" % basefile
baseoutfile = os.path.basename(outfile)
outdir = os.path.dirname(outfile)
if infile.endswith(".remote"):
for line in IOTools.open_file(infile):
repo, acc = line.strip().split("\t")[:2]
if repo == "SRA":
if not os.path.isfile(outfile + ".1.gz"):
statement = "; ".join(
[Sra.prefetch(acc),
Sra.extract(acc, outdir)])
P.run(statement)
else:
pass
elif repo == "GDC":
base = os.path.splitext(basefile)
outfile = "bam.dir/" + base[0] + ".bam"
token = glob.glob("gdc-user-token*")
if len(token) > 0:
token = token[0]
else:
token = None
s, infile = Sra.process_remote_BAM(
infile,
token,
filename,
filter_bed=os.path.join(
PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs_bed"]))
infile = " ".join(infile)
if not os.path.isfile(outfile):
statement = "; ".join([
"mkdir -p %(filename)s", s,
'''cp %(infile)s %(outfile)s;
rm -r %(filename)s'''
])
P.run(statement)
else:
pass
else:
raise ValueError("Unknown repository: %s" % repo)
else:
pass
def assembleWithStringTie(infiles, outfile):
infile, reference = infiles
basefile = os.path.basename(infile)
job_threads = PARAMS["stringtie_threads"]
job_memory = PARAMS["stringtie_memory"]
tmpfile = P.get_temp_filename()
if os.path.exists(tmpfile):
os.unlink(tmpfile)
statement = '''
portcullis full
-t 1
-o portcullis/%(basefile)s/
-r %(portcullis_bedref)s
-b
%(portcullis_fastaref)s
%(infile)s &&
mv portcullis/%(basefile)s/portcullis.filtered.bam %(tmpfile)s &&
rm -r portcullis/%(basefile)s/ &&
stringtie %(tmpfile)s
-p %(stringtie_threads)s
-G <(zcat %(reference)s)
%(stringtie_options)s
2> %(outfile)s.log
| gzip > %(outfile)s &&
rm %(tmpfile)s'''
if infile.endswith(".remote"):
token = glob.glob("gdc-user-token*")
tmpfilename = P.get_temp_filename()
if os.path.exists(tmpfilename):
os.unlink(tmpfilename)
if len(token) > 0:
token = token[0]
else:
token = None
s, infile = Sra.process_remote_BAM(
infile,
token,
tmpfilename,
filter_bed=os.path.join(
PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs_bed"]))
infile = " ".join(infile)
statement = "; ".join([
"mkdir -p %(tmpfilename)s", s, statement, "rm -r %(tmpfilename)s"
])
P.run(statement)
def quantifyWithSalmon(infiles, outfile):
'''Quantify existing samples against genesets'''
job_threads = 2
job_memory = "8G"
infile, gtffile = infiles
basefile = os.path.basename(infile)
gtfbase = P.snip(os.path.basename(gtffile), ".gz")
salmonIndex = "salmon_index/" + gtfbase + ".salmon.index"
fastq1 = P.snip(outfile, "_agg-agg-agg") + ".1.fastq"
fastq2 = P.snip(outfile, "_agg-agg-agg") + ".2.fastq"
salmon_options = PARAMS["salmon_quantoptions"]
statement = '''
samtools fastq
-1 %(fastq1)s
-2 %(fastq2)s
%(infile)s;
salmon quant -i %(salmonIndex)s
--libType A
-1 %(fastq1)s
-2 %(fastq2)s
-o %(outfile)s
--threads %(job_threads)s
%(salmon_options)s;
checkpoint;
mv %(outfile)s/quant.sf %(outfile)s.sf;
rm %(fastq1)s; rm %(fastq2)s
'''
if infile.endswith(".remote"):
token = glob.glob("gdc-user-token*")
filename = "temp_bams/%s" % basefile
tmpfilename = P.getTempFilename()
if len(token) > 0:
token = token[0]
else:
token = None
s, infile = Sra.process_remote_BAM(
infile,
token,
filename,
filter_bed=os.path.join(
PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs_bed"]))
infile = " ".join(infile)
statement = "; checkpoint; ".join(
["mkdir %(filename)s", s, statement, "rm -r %(filename)s"])
P.run()
def runKalistoOnRemoteBAM(infiles, outfile):
'''running kalisto on .bam or .remote files'''
job_memory="6G"
infile, kallisto_index = infiles
outdir = os.path.dirname(outfile)
outfile = P.snip(outfile, ".gz")
statement = []
tempfastq1 = P.getTempFilename()
tempfastq2 = P.getTempFilename()
rm_files = [tempfastq1, tempfastq2]
if infile.endswith(".remote"):
tempbam = P.getTempFilename()
s, infiles = Sra.process_remote_BAM(infile, outdir=tempbam)
infile = " ".join(infiles)
statement.append(s)
rm_files.append(tempbam)
statement.append('''samtools fastq %(infile)s
-1 %(tempfastq1)s
-2 %(tempfastq2)s''')
statement.append('''kallisto quant -i %(kallisto_index)s
-o %(outdir)s
%(tempfastq1)s %(tempfastq2)s''')
rm_files = " ".join(rm_files)
statement.append('''rm -R %(rm_files)s''')
statement.append('''gzip %(outfile)s''')
statement = "; \n checkpoint;\n".join(statement)
P.run()