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bcftbx/mock: updates for Python 3 compatibility #121

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merged 2 commits into from Sep 11, 2019
Merged

bcftbx/mock: updates for Python 3 compatibility #121

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636e685
bcftbx/mock: switch from 'xrange' to Python3-compatible 'range' funct…
pjbriggs Sep 11, 2019
5a04c0f
bcftbx/mock: write correct type of data for mock gzipped files.
pjbriggs Sep 11, 2019
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21 changes: 11 additions & 10 deletions bcftbx/mock.py
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Expand Up @@ -37,6 +37,7 @@
from .TabFile import TabFile
from .utils import OrderedDictionary
from .utils import mkdir
from builtins import range

#######################################################################
# Module data
Expand Down Expand Up @@ -165,7 +166,7 @@ def create(run_name,bases_mask,nlanes,tilecount=None,
# AlignToPhiX
if align_to_phix:
xml += " <AlignToPhiX>\n"
for i in xrange(nlanes):
for i in range(nlanes):
xml += " <Lane>%s</Lane>\n" % (i+1)
xml += " </AlignToPhiX>\n"
# Footer
Expand Down Expand Up @@ -519,7 +520,7 @@ def lanes(self):
"""
List of lane numbers
"""
return [l for l in xrange(1,self._nlanes+1)]
return [l for l in range(1,self._nlanes+1)]

@property
def dirn(self):
Expand Down Expand Up @@ -568,16 +569,16 @@ def create(self):
mkdir(self._path('Data','Intensities'))
mkdir(self._path('Data','Intensities','BaseCalls'))
# Lanes
for i in xrange(1,nlanes+1):
for i in range(1,nlanes+1):
# .locs files
mkdir(self._path('Data','Intensities','L%03d' % i))
for j in xrange(1101,1101+ntiles):
for j in range(1101,1101+ntiles):
io.open(self._path('Data','Intensities','L%03d' % i,
's_%d_%d.locs' % (i,j)),'wb+').close()
# BaseCalls directory
mkdir(self._path('Data','Intensities','BaseCalls',
'L%03d' % i))
for j in xrange(1101,1101+ntiles):
for j in range(1101,1101+ntiles):
if self._include_control:
# Add .control files
io.open(self._path('Data',
Expand All @@ -596,7 +597,7 @@ def create(self):
# No cycle subdirectores (e.g. 'C121.1')
# so put bcl files directory in lane directory
# This is the case for NextSeq
for j in xrange(1,ntiles+1):
for j in range(1,ntiles+1):
io.open(self._path('Data',
'Intensities',
'BaseCalls',
Expand All @@ -611,13 +612,13 @@ def create(self):
'%04d%s.bci' % (j,bcl_ext)),'wb+').close()
# Cycles subdirectories
if self._include_cycles:
for k in xrange(1,ncycles+1):
for k in range(1,ncycles+1):
mkdir(self._path('Data',
'Intensities',
'BaseCalls',
'L%03d' % i,
'C%d.1' % k))
for j in xrange(1101,1101+ntiles):
for j in range(1101,1101+ntiles):
# .bcl files
io.open(self._path('Data',
'Intensities',
Expand Down Expand Up @@ -1167,11 +1168,11 @@ def _touch(self,f):
if f.endswith(".gz"):
# Make empty gzipped file
with gzip.open(f,'wb') as fp:
fp.write("")
fp.write(b"")
else:
# Make regular empty file
with io.open(f,'wb') as fp:
fp.write("")
fp.write(b"")

def remove(self):
"""Delete the directory structure and contents
Expand Down