def make_protein_coding_gtf(self):
with open("%s/protein_coding.gtf" % brp.configs().exp_dir, "a") as f:
for line in open(brp.configs().genome_gtf):
if "##" in line:
print(line, end="", file=f)
else:
if "protein_coding" in line:
print(line, end="", file=f)
def make_protein_coding_gtf(self):
with open('%s/protein_coding.gtf' % brp.configs().exp_dir, 'a') as f:
for line in open(brp.configs().genome_gtf):
if "##" in line:
print(line, end='', file=f)
else:
if 'protein_coding' in line:
print(line, end='', file=f)
def run(self):
try:
os.makedirs(self.eisa_dir)
except OSError:
pass
with open('%s/exons.gtf' % self.eisa_dir, 'a') as f:
for line in open(brp.configs().genome_gtf):
if "##" in line:
print(line, end='', file=f)
else:
cols = line.split()
if cols[2] == 'exon':
print(line, end='', file=f)
def run(self):
try:
os.makedirs(self.eisa_dir)
except OSError:
pass
with open('%s/exons.gtf' % self.eisa_dir, 'a') as f:
for line in open(brp.configs().genome_gtf):
if "##" in line:
print(line, end='', file=f)
else:
cols = line.split()
if cols[2] == 'exon':
print(line, end='', file=f)
class extract_exon_annotation(luigi.Task):
'''extract only exons from annotation file,
will be used to filter reads that align to an intron
'''
eisa_dir = '%s/eisa' % brp.configs().exp_dir
def run(self):
try:
os.makedirs(self.eisa_dir)
except OSError:
pass
with open('%s/exons.gtf' % self.eisa_dir, 'a') as f:
for line in open(brp.configs().genome_gtf):
if "##" in line:
print(line, end='', file=f)
else:
cols = line.split()
if cols[2] == 'exon':
print(line, end='', file=f)
def output(self):
return luigi.LocalTarget('%s/exons.gtf' % self.eisa_dir)
def output(self):
return luigi.LocalTarget("%s/protein_coding.gtf" % brp.configs().exp_dir)
def run(self):
try:
self.make_protein_coding_gtf()
except FileNotFoundError:
os.makedirs(brp.configs().exp_dir)
self.make_protein_coding_gtf()
def output_dir(self):
return '%s/fastqc' % brp.configs().exp_dir
def output_dir(self):
return '%s/eisa/%s' % (brp.configs().exp_dir, self.sample)
def output(self):
return luigi.LocalTarget('%s/protein_coding.gtf' %
brp.configs().exp_dir)
def run(self):
try:
self.make_protein_coding_gtf()
except FileNotFoundError:
os.makedirs(brp.configs().exp_dir)
self.make_protein_coding_gtf()
def output_dir(self):
return '%s/eisa/%s' % (brp.configs().exp_dir, self.sample)
