def get_mapped_filtered_filename(self, fragment, **kwargs):
'''Get the filename of the reads mapped to patient initial reference'''
from hivwholeseq.patients.filenames import get_mapped_filtered_filename as gfn
pname = self.patientname
samplename_pat = self['patient sample']
PCR = int(self.PCR)
return gfn(pname, samplename_pat, fragment, PCR=PCR, **kwargs)
def get_mapped_filtered_filename(self, fragment, **kwargs):
'''Get the filename of the reads mapped to patient initial reference'''
from hivwholeseq.patients.filenames import get_mapped_filtered_filename as gfn
pname = self.patientname
samplename_pat = self['patient sample']
PCR = int(self.PCR)
return gfn(pname, samplename_pat, fragment, PCR=PCR, **kwargs)
def get_consensus_filename(self, fragment, **kwargs):
'''Get the filename of the consensus'''
from hivwholeseq.sequencing.filenames import get_consensus_filename as gfn
from hivwholeseq.sequencing.filenames import get_merged_consensus_filename as gfn2
if fragment != 'genomewide':
return gfn(self.folder, adaID=None, fragment=fragment, **kwargs)
else:
return gfn2(self.folder, adaID=None, **kwargs)
def get_consensus_filename(self, fragment, **kwargs):
'''Get the filename of the consensus'''
from hivwholeseq.sequencing.filenames import get_consensus_filename as gfn
from hivwholeseq.sequencing.filenames import get_merged_consensus_filename as gfn2
if fragment != 'genomewide':
return gfn(self.folder, adaID=None, fragment=fragment, **kwargs)
else:
return gfn2(self.folder, adaID=None, **kwargs)
def get_mapped_filename(self, fragment, **kwargs):
'''Get the filename of the mapped reads'''
from hivwholeseq.sequencing.filenames import get_mapped_filename as gfn
return gfn(self.folder, adaID=None, fragment=fragment, **kwargs)
def get_premapped_filename(self, **kwargs):
'''Get the filename of the readed premapped to reference'''
from hivwholeseq.sequencing.filenames import get_premapped_filename as gfn
return gfn(self.folder, **kwargs)
def get_reference_premap_filename(self, **kwargs):
'''Get the filename of the premapping refernce'''
from hivwholeseq.sequencing.filenames import get_reference_premap_filename as gfn
return gfn(self.seqrun_folder, self.adapter, **kwargs)
def get_read_filenames(self, **kwargs):
'''Get the filenames of the demultiplexed reads'''
from hivwholeseq.sequencing.filenames import get_read_filenames as gfn
return gfn(self.folder, **kwargs)
def get_mapped_filename(self, fragment, **kwargs):
'''Get the filename of the mapped reads'''
from hivwholeseq.sequencing.filenames import get_mapped_filename as gfn
return gfn(self.folder, adaID=None, fragment=fragment, **kwargs)
def get_premapped_filename(self, **kwargs):
'''Get the filename of the readed premapped to reference'''
from hivwholeseq.sequencing.filenames import get_premapped_filename as gfn
return gfn(self.folder, **kwargs)
def get_reference_premap_filename(self, **kwargs):
'''Get the filename of the premapping refernce'''
from hivwholeseq.sequencing.filenames import get_reference_premap_filename as gfn
return gfn(self.seqrun_folder, self.adapter, **kwargs)
def get_read_filenames(self, **kwargs):
'''Get the filenames of the demultiplexed reads'''
from hivwholeseq.sequencing.filenames import get_read_filenames as gfn
return gfn(self.folder, **kwargs)