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Cython: Sequence objects: repr() method now returns a Fasta or Fastq

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Celine Mercier
2018-10-17 16:53:42 +02:00
parent b027762059
commit 4802e32f72
1 changed files with 11 additions and 0 deletions
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11
python/obitools3/dms/obiseq.pyx
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@ -16,6 +16,10 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
from .capi.obiutils cimport reverse_complement_sequence from .capi.obiutils cimport reverse_complement_sequence
from obitools3.format.fasta import FastaFormat
from obitools3.format.fastq import FastqFormat
from cpython cimport array from cpython cimport array
import array import array
from copy import deepcopy from copy import deepcopy
@ -414,3 +418,10 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
def __len__(self): def __len__(self):
return len(self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index)) return len(self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index))
def __repr__(self):
if self.quality is None:
formatter = FastaFormat()
else:
formatter = FastqFormat()
return bytes2str(formatter(self))