#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import gzip
from singlecellmultiomics.pyutils.handlelimiter import HandleLimiter
[docs]class FastqHandle:
def __init__(
self,
path,
pairedEnd=False,
single_cell=False,
maxHandles=500):
self.pe = pairedEnd
self.sc = single_cell
self.path = path
if not self.sc:
if pairedEnd:
self.handles = [
gzip.open(
path +
'R1.fastq.gz',
'wt',compresslevel=1),
gzip.open(
path +
'R2.fastq.gz',
'wt',compresslevel=1)]
else:
self.handles = [gzip.open(path + 'reads.fastq.gz', 'wt')]
else:
self.handles = HandleLimiter(
compressionLevel=1, maxHandles=maxHandles)
[docs] def write(self, records):
if self.sc:
for readIdx, record in zip(('R1', 'R2'), records):
# Obtain cell from record:
cell = f"{record.tags.get('bi','no_cell_id')}.{record.tags.get('MX','unk')}"
self.handles.write(
f'{self.path}.{cell}.{readIdx}.fastq.gz',
str(record),
method=1)
else:
for handle, record in zip(self.handles, records):
handle.write(str(record))
[docs] def close(self):
if self.sc:
self.handles.close()
else:
for handle in self.handles:
handle.close()