def set_meta( self, dataset, **kwd ):
Text.set_meta(self, dataset, **kwd )
data_dir = dataset.extra_files_path
## search data_dir/genome_version for files
regulation_pattern = 'regulation_(.+).bin'
# annotation files that are included in snpEff by a flag
annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
regulations = []
annotations = []
if data_dir and os.path.isdir(data_dir):
for root, dirs, files in os.walk(data_dir):
for fname in files:
if fname.startswith('snpEffectPredictor'):
# if snpEffectPredictor.bin download succeeded
genome_version = os.path.basename(root)
dataset.metadata.genome_version = genome_version
else:
m = re.match(regulation_pattern,fname)
if m:
name = m.groups()[0]
regulations.append(name)
elif fname in annotations_dict:
value = annotations_dict[fname]
name = value.lstrip('-')
annotations.append(name)
dataset.metadata.regulation = regulations
dataset.metadata.annotation = annotations
def set_meta(self, dataset, **kwd):
Text.set_meta(self, dataset, **kwd)
data_dir = dataset.extra_files_path
# search data_dir/genome_version for files
regulation_pattern = 'regulation_(.+).bin'
# annotation files that are included in snpEff by a flag
annotations_dict = {
'nextProt.bin': '-nextprot',
'motif.bin': '-motif',
'interactions.bin': '-interaction'
}
regulations = []
annotations = []
genome_version = None
snpeff_version = None
if data_dir and os.path.isdir(data_dir):
for root, dirs, files in os.walk(data_dir):
for fname in files:
if fname.startswith('snpEffectPredictor'):
# if snpEffectPredictor.bin download succeeded
genome_version = os.path.basename(root)
dataset.metadata.genome_version = genome_version
# read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version
snpeff_version = self.getSnpeffVersionFromFile(
os.path.join(root, fname))
if snpeff_version:
dataset.metadata.snpeff_version = snpeff_version
else:
m = re.match(regulation_pattern, fname)
if m:
name = m.groups()[0]
regulations.append(name)
elif fname in annotations_dict:
value = annotations_dict[fname]
name = value.lstrip('-')
annotations.append(name)
dataset.metadata.regulation = regulations
dataset.metadata.annotation = annotations
try:
with open(dataset.file_name, 'w') as fh:
fh.write(
"%s\n" %
genome_version if genome_version else 'Genome unknown')
fh.write("%s\n" % snpeff_version
if snpeff_version else 'SnpEff version unknown')
if annotations:
fh.write("annotations: %s\n" % ','.join(annotations))
if regulations:
fh.write("regulations: %s\n" % ','.join(regulations))
except Exception:
pass
def set_meta( self, dataset, **kwd ):
Text.set_meta(self, dataset, **kwd )
data_dir = dataset.extra_files_path
# search data_dir/genome_version for files
regulation_pattern = 'regulation_(.+).bin'
# annotation files that are included in snpEff by a flag
annotations_dict = {'nextProt.bin' : '-nextprot', 'motif.bin': '-motif'}
regulations = []
annotations = []
genome_version = None
snpeff_version = None
if data_dir and os.path.isdir(data_dir):
for root, dirs, files in os.walk(data_dir):
for fname in files:
if fname.startswith('snpEffectPredictor'):
# if snpEffectPredictor.bin download succeeded
genome_version = os.path.basename(root)
dataset.metadata.genome_version = genome_version
# read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version
snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root, fname))
if snpeff_version:
dataset.metadata.snpeff_version = snpeff_version
else:
m = re.match(regulation_pattern, fname)
if m:
name = m.groups()[0]
regulations.append(name)
elif fname in annotations_dict:
value = annotations_dict[fname]
name = value.lstrip('-')
annotations.append(name)
dataset.metadata.regulation = regulations
dataset.metadata.annotation = annotations
try:
fh = file(dataset.file_name, 'w')
fh.write("%s\n" % genome_version if genome_version else 'Genome unknown')
fh.write("%s\n" % snpeff_version if snpeff_version else 'SnpEff version unknown')
if annotations:
fh.write("annotations: %s\n" % ','.join(annotations))
if regulations:
fh.write("regulations: %s\n" % ','.join(regulations))
fh.close()
except:
pass
def set_meta(self, dataset, **kwd):
Text.set_meta(self, dataset, **kwd)
data_dir = dataset.extra_files_path
## search data_dir/genome_version for files
regulation_pattern = "regulation_(.+).bin"
# annotation files that are included in snpEff by a flag
annotations_dict = {"nextProt.bin": "-nextprot", "motif.bin": "-motif"}
regulations = []
annotations = []
if data_dir and os.path.isdir(data_dir):
for root, dirs, files in os.walk(data_dir):
for fname in files:
if fname.startswith("snpEffectPredictor"):
# if snpEffectPredictor.bin download succeeded
genome_version = os.path.basename(root)
dataset.metadata.genome_version = genome_version
else:
m = re.match(regulation_pattern, fname)
if m:
name = m.groups()[0]
regulations.append(name)
elif fname in annotations_dict:
value = annotations_dict[fname]
name = value.lstrip("-")
annotations.append(name)
dataset.metadata.regulation = regulations
dataset.metadata.annotation = annotations
try:
fh = file(dataset.file_name, "w")
fh.write("%s\n" % genome_version)
if annotations:
fh.write("annotations: %s\n" % ",".join(annotations))
if regulations:
fh.write("regulations: %s\n" % ",".join(regulations))
fh.close()
except:
pass
