def run_stringtie_expression(data):
"""
estimate expression from Stringtie, using the bcbio datadict
does not do transcriptome assembly
"""
bam = dd.get_work_bam(data)
sample_name = dd.get_sample_name(data)
out_dir = os.path.join("stringtie", sample_name)
isoform_fpkm = os.path.join(out_dir, sample_name + ".isoform.fpkm")
gene_fpkm = os.path.join(out_dir, sample_name + ".fpkm")
assembly = os.path.abspath(os.path.join(out_dir, "stringtie-assembly.gtf"))
if file_exists(isoform_fpkm) and file_exists(gene_fpkm):
data = dd.set_stringtie_dir(data, out_dir)
data = dd.set_fpkm(data, gene_fpkm)
data = dd.set_fpkm_isoform(data, isoform_fpkm)
if "stringtie" in dd.get_transcript_assembler(data):
assembled_gtfs = dd.get_assembled_gtf(data)
assembled_gtfs.append(assembly)
data = dd.set_assembled_gtf(data, assembled_gtfs)
return data
with file_transaction(data, out_dir) as tx_out_dir:
transcript_file = _stringtie_expression(bam, data, tx_out_dir)
df = _parse_ballgown(transcript_file)
_write_fpkms(df, tx_out_dir, sample_name)
data = dd.set_stringtie_dir(data, out_dir)
data = dd.set_fpkm(data, gene_fpkm)
data = dd.set_fpkm_isoform(data, isoform_fpkm)
if "stringtie" in dd.get_transcript_assembler(data):
assembled_gtfs = dd.get_assembled_gtf(data)
assembled_gtfs.append(assembly)
data = dd.set_assembled_gtf(data, assembled_gtfs)
return data
def run_stringtie_expression(data):
"""
estimate expression from Stringtie, using the bcbio datadict
does not do transcriptome assembly
"""
bam = dd.get_work_bam(data)
sample_name = dd.get_sample_name(data)
out_dir = os.path.join("stringtie", sample_name)
isoform_fpkm = os.path.join(out_dir, sample_name + ".isoform.fpkm")
gene_fpkm = os.path.join(out_dir, sample_name + ".fpkm")
assembly = os.path.abspath(os.path.join(out_dir, "stringtie-assembly.gtf"))
if file_exists(isoform_fpkm) and file_exists(gene_fpkm):
data = dd.set_stringtie_dir(data, out_dir)
data = dd.set_fpkm(data, gene_fpkm)
data = dd.set_fpkm_isoform(data, isoform_fpkm)
if "stringtie" in dd.get_transcript_assembler(data):
assembled_gtfs = dd.get_assembled_gtf(data)
assembled_gtfs.append(assembly)
data = dd.set_assembled_gtf(data, assembled_gtfs)
return data
with file_transaction(data, out_dir) as tx_out_dir:
transcript_file = _stringtie_expression(bam, data, tx_out_dir)
df = _parse_ballgown(transcript_file)
_write_fpkms(df, tx_out_dir, sample_name)
data = dd.set_stringtie_dir(data, out_dir)
data = dd.set_fpkm(data, gene_fpkm)
data = dd.set_fpkm_isoform(data, isoform_fpkm)
if "stringtie" in dd.get_transcript_assembler(data):
assembled_gtfs = dd.get_assembled_gtf(data)
assembled_gtfs.append(assembly)
data = dd.set_assembled_gtf(data, assembled_gtfs)
return data