__version__ = "v1.0"
__copyright__ = "Copyright 2022"
__license__ = "MIT"
__lab__ = "Adam Cribbs lab"
import gzip
import pandas as pd
from functools import wraps
from resimpy.util.file.create.Folder import folder as crtfolder
[docs]class write(object):
def __init__(self):
self.crtfolder = crtfolder()
def __call__(self, deal):
generic = self.generic
excel = self.excel
@wraps(deal)
def write(ph, *args, **kwargs):
res = deal(ph, **kwargs)
keys = [*kwargs.keys()]
if kwargs['type'] == 'generic':
generic(
df=kwargs['df'],
sv_fpn=kwargs['sv_fpn'],
df_sep='\t' if 'df_sep' not in keys else kwargs['df_sep'],
id_from=0 if 'id_from' not in keys else kwargs['id_from'],
header=None if 'header' not in keys else kwargs['header'],
index=False if 'index' not in keys else kwargs['index'],
)
elif kwargs['type'] == 'excel':
excel(
df=kwargs['df'],
sv_fpn=kwargs['sv_fpn'],
sheet_name='Sheet1' if 'sheet_name' not in keys else kwargs['sheet_name'],
id_from=0 if 'id_from' not in keys else kwargs['id_from'],
header=None if 'header' not in keys else kwargs['header'],
index=False if 'index' not in keys else kwargs['index'],
)
return res
return write
[docs] def togz(self, list_2d, sv_fp, fn, symbol='_'):
self.crtfolder.osmkdir(sv_fp)
fname = sv_fp + fn + '.fastq.gz'
f = gzip.open(fname, 'wt')
for i, read in enumerate(list_2d):
seq = str(read[0])
# print('No.{} saving in FASTQ format.'.format(i + 1))
f.write('@' + symbol.join(read[1:]) + '\n')
f.write(seq + '\n')
f.write('+' + '\n')
f.write('s' * len(seq) + '\n')
f.close()
return 0
[docs] def generic(self, df, sv_fpn, df_sep='\t', header=None, index=False, id_from=0):
df_ = pd.DataFrame(df)
df_.index = df_.index + id_from
return df_.to_csv(
sv_fpn,
sep=df_sep,
header=header,
index=index
)
[docs] def excel(self, df, sv_fpn=None, sheet_name='Sheet1', header=None, index=False, id_from=0):
df_ = pd.DataFrame(df)
df_.index = df_.index + id_from
return df_.to_excel(
sv_fpn,
sheet_name=sheet_name,
header=header,
index=index
)