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)
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)