class CCSInput(object):
"""
Wrapper class for handling multiple formats specifying CCS sequences.
The old convention was to use .fasta, but we would like to be able to pass
the classifier a ConsensusReadSet (i.e. .bam files) instead for use within
pbsmrtpipe.
"""
def __init__(self, file_name):
self.file_name = file_name
self._is_fasta = False
self.ext = op.splitext(file_name)[1].upper()
if self.ext in [".FA", ".FASTA"]:
self._dataset = FastaReader(file_name)
self._is_fasta = True
elif self.ext == ".BAM":
self._dataset = openDataFile(file_name)
else: # either contigset.xml or consensusreadset.xml
assert self.ext == ".XML"
self._dataset = openDataSet(file_name)
if isinstance(self._dataset, ContigSet):
self._is_fasta = True
def __iter__(self):
for rec in self._dataset:
if not self._is_fasta:
rec = CCSBamSequence(rec.peer)
yield rec
def close(self):
"""Close all datasets."""
self._dataset.close()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
def __len__(self):
if not self._is_fasta:
return len(self._dataset)
else:
if self.ext in [".FA", ".FASTA"]:
return len([r for r in FastaReader(self.file_name)])
else: # contigset
n = 0
for rr in self._dataset.resourceReaders():
n += len([r for r in rr])
return n
def __delitem__(self, dummy_name):
raise NotImplementedError("%s.%s" %
(self.__class__.__name__, "__delitem__"))
def __setitem__(self, dummy_index, dummy_name):
raise NotImplementedError("%s.%s" %
(self.__class__.__name__, "__setitem__"))
def __getitem__(self, key):
raise NotImplementedError("%s.%s" %
(self.__class__.__name__, "__getitem__"))
class CCSInput(object):
"""
Wrapper class for handling multiple formats specifying CCS sequences.
The old convention was to use .fasta, but we would like to be able to pass
the classifier a ConsensusReadSet (i.e. .bam files) instead for use within
pbsmrtpipe.
"""
def __init__(self, file_name):
self.file_name = file_name
self._is_fasta = False
self.ext = op.splitext(file_name)[1].upper()
if self.ext in [".FA", ".FASTA"]:
self._dataset = FastaReader(file_name)
self._is_fasta = True
elif self.ext == ".BAM":
self._dataset = openDataFile(file_name)
else: # either contigset.xml or consensusreadset.xml
assert self.ext == ".XML"
self._dataset = openDataSet(file_name)
if isinstance(self._dataset, ContigSet):
self._is_fasta = True
def __iter__(self):
for rec in self._dataset:
if not self._is_fasta:
rec = CCSBamSequence(rec.peer)
yield rec
def close(self):
"""Close all datasets."""
self._dataset.close()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
def __len__(self):
if not self._is_fasta:
return len(self._dataset)
else:
if self.ext in [".FA", ".FASTA"]:
return len([r for r in FastaReader(self.file_name)])
else: # contigset
n = 0
for rr in self._dataset.resourceReaders():
n += len([r for r in rr])
return n
def __delitem__(self, dummy_name):
raise NotImplementedError("%s.%s" % (self.__class__.__name__,
"__delitem__"))
def __setitem__(self, dummy_index, dummy_name):
raise NotImplementedError("%s.%s" % (self.__class__.__name__,
"__setitem__"))
def __getitem__(self, key):
raise NotImplementedError("%s.%s" % (self.__class__.__name__,
"__getitem__"))
#! /usr/bin/env python
import sys
from pbcore.io import FastaReader
f = FastaReader(sys.argv[1])
for seq in f:
chr = seq
list = chr.sequence.split('N')
max = 0
max_seq = ""
for sec in list:
if len(sec) > max:
max = len(sec)
max_seq = sec
print len(max_seq)
wf = open("human_chr14.fa","w")
wf.write(max_seq)
f.close()
wf.close()
#! /usr/bin/env python
import sys
from pbcore.io import FastaReader
f = FastaReader(sys.argv[1])
for seq in f:
chr = seq
list = chr.sequence.split('N')
max = 0
max_seq = ""
for sec in list:
if len(sec) > max:
max = len(sec)
max_seq = sec
print len(max_seq)
wf = open("human_chr14.fa", "w")
wf.write(max_seq)
f.close()
wf.close()
