def addTestFile(self, field='ind_id', file_pat='/mnt/scratch/asalomatov/data/SSC/wes/feature_sets/fb/all_SNP/%s'):
num_subst = len(re.findall('\%s', file_pat))
print('%s substitutions found' % num_subst)
if num_subst > 0:
x = self.ped[field].apply(lambda f: func.listFiles(file_pat % ((f,) * num_subst)))
self.ped['test'] = pd.Series(x, index=self.ped.index)
else:
self.ped['test'] = file_pat
def addBai(self, field='ind_id', file_pat='/mnt/ceph/asalomatov/SSC_Eichler/data_S3/%s*bam.bai'):
num_subst = len(re.findall('\%s', file_pat))
print('%s substitutions found' % num_subst)
if num_subst > 0:
x = self.ped[field].apply(lambda f: func.listFiles(file_pat % ((f,) * num_subst)))
self.ped['bai'] = pd.Series(x, index=self.ped.index)
else:
self.ped['bai'] = file_pat
def addBai(self,
field='ind_id',
file_pat='/mnt/ceph/asalomatov/SSC_Eichler/data_S3/%s*bam.bai'):
num_subst = len(re.findall('\%s', file_pat))
print('%s substitutions found' % num_subst)
if num_subst > 0:
x = self.ped[field].apply(
lambda f: func.listFiles(file_pat % ((f, ) * num_subst)))
self.ped['bai'] = pd.Series(x, index=self.ped.index)
else:
self.ped['bai'] = file_pat
def addTestFile(
self,
field='ind_id',
file_pat='/mnt/scratch/asalomatov/data/SSC/wes/feature_sets/fb/all_SNP/%s'
):
num_subst = len(re.findall('\%s', file_pat))
print('%s substitutions found' % num_subst)
if num_subst > 0:
x = self.ped[field].apply(
lambda f: func.listFiles(file_pat % ((f, ) * num_subst)))
self.ped['test'] = pd.Series(x, index=self.ped.index)
else:
self.ped['test'] = file_pat
def addBam(self,
field='ind_id',
file_pat='/mnt/ceph/asalomatov/SSC_Eichler/data_S3/%s*.bam',
num_subst=2):
"""Sometimes it is easier to add a bam column using a sting substitution
pattern. Usually it is done manually"""
num_subst = len(findall('\%s', file_pat))
print num_subst, ' substitutions found'
if num_subst > 0:
x = self.ped[field].apply(
lambda f: func.listFiles(file_pat % ((f, ) * num_subst)))
self.ped['bam'] = pd.Series(x, index=self.ped.index)
else:
self.ped['bam'] = file_pat